diff --git a/gui/tests/env.js b/gui/tests/env.js
index eef93eb2081037b4b6eb8cb950aaa74254b496a8..1229b90c75f549bce4b06c4d23061fcd49ed45e1 100644
--- a/gui/tests/env.js
+++ b/gui/tests/env.js
@@ -2077,7 +2077,7 @@ window.nomadEnv = {
"name": "parsers/edmft",
"description": "NOMAD parser for EDMFT.",
"plugin_package": "electronicparsers",
- "level": 0,
+ "level": 2,
"aliases": [
"parsers/edmft"
],
@@ -2220,7 +2220,7 @@ window.nomadEnv = {
"name": "parsers/magres",
"description": "NOMAD parser for MAGRES.",
"plugin_package": "electronicparsers",
- "level": 0,
+ "level": 1,
"aliases": [
"parsers/magres"
],
@@ -2481,7 +2481,7 @@ window.nomadEnv = {
"name": "parsers/tbstudio",
"description": "NOMAD parser for TBSTUDIO.",
"plugin_package": "electronicparsers",
- "level": 0,
+ "level": 1,
"aliases": [
"parsers/tbstudio"
],
@@ -2533,7 +2533,7 @@ window.nomadEnv = {
"name": "parsers/w2dynamics",
"description": "NOMAD parser for W2DYNAMICS.",
"plugin_package": "electronicparsers",
- "level": 0,
+ "level": 2,
"aliases": [
"parsers/w2dynamics"
],
@@ -2555,7 +2555,7 @@ window.nomadEnv = {
"name": "parsers/wannier90",
"description": "NOMAD parser for WANNIER90.",
"plugin_package": "electronicparsers",
- "level": 0,
+ "level": 1,
"aliases": [
"parsers/wannier90"
],
diff --git a/nomad/app/v1/routers/systems.py b/nomad/app/v1/routers/systems.py
index 36748041d27430c43d74e9282662dcbcd449a1be..8c7e375aa9563d1e1a76590d6ca7576591014230 100644
--- a/nomad/app/v1/routers/systems.py
+++ b/nomad/app/v1/routers/systems.py
@@ -26,15 +26,12 @@ from fastapi import APIRouter, Depends, Path, Query, status, HTTPException
from fastapi.responses import Response
import ase.io
import ase.build
-from MDAnalysis.lib.util import NamedStream
-from MDAnalysis.coordinates.PDB import PDBWriter
from nomad.units import ureg
from nomad.utils import strip, deep_get, query_list_to_dict
from nomad.atomutils import Formula, wrap_positions, unwrap_positions
from nomad.normalizing.common import (
ase_atoms_from_nomad_atoms,
- mda_universe_from_nomad_atoms,
)
from nomad.datamodel.metainfo.system import Atoms as NOMADAtoms
from .entries import answer_entry_archive_request
@@ -72,36 +69,16 @@ def write_pdb(atoms: NOMADAtoms, entry_id: str = None, formula: str = None) -> s
lines.append(
f'REMARK 285 C: {cell[2, 0]:.3f}, {cell[2, 1]:.3f}, {cell[2, 2]:.3f}\n'
)
- else:
- lines.append(
- 'REMARK 285 UNITARY VALUES FOR THE UNIT CELL SET BECAUSE UNIT CELL INFORMATION\n'
- )
- lines.append(
- 'REMARK 285 WAS MISSING. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1\n'
- )
- lines.append(
- 'REMARK 285 RECORD IS INCLUDED, BUT THE VALUES ON THIS RECORD ARE MEANINGLESS.\n'
- )
if pbc is not None:
pbc = ['TRUE' if x else 'FALSE' for x in pbc]
lines.append(f'REMARK 285 PBC (A, B, C): {pbc[0]}, {pbc[1]}, {pbc[2]}\n')
- mda_string_stream = StringIO()
- mda_named_stream = NamedStream(
- mda_string_stream, f'temp.{format}', close=False, reset=False
- )
- writer = PDBWriter(mda_named_stream, remarks='')
- universe = mda_universe_from_nomad_atoms(atoms)
- writer.write(universe)
- writer.close()
-
- # We skip the title line that is written by MDA (cannot be disabled otherwise)
- mda_string_stream.seek(0)
- for line in mda_string_stream.readlines():
- if not line.startswith(('REMARK', 'TITLE')):
- lines.append(line)
-
+ stream = StringIO()
+ atoms = ase_atoms_from_nomad_atoms(atoms)
+ ase.io.write(stream, atoms, format='proteindatabank')
+ stream.seek(0)
content = ''.join(lines)
+ content += stream.read()
return content
diff --git a/nomad/atomutils.py b/nomad/atomutils.py
index c95aab394953d144f510fe5a461ff744d8eb9477..07e9959918b2373c75426b692d8cd765d50c5c86 100644
--- a/nomad/atomutils.py
+++ b/nomad/atomutils.py
@@ -23,16 +23,11 @@ import itertools
import logging
import math
import re
-import warnings
-from array import array
-from collections import namedtuple
from functools import reduce
-from itertools import chain
from string import ascii_uppercase
from typing import (
TYPE_CHECKING,
Any,
- Callable,
Dict,
Iterable,
List,
@@ -43,27 +38,15 @@ from typing import (
import ase.data
import ase.geometry
-import MDAnalysis
-import MDAnalysis.analysis.rdf as MDA_RDF
-import networkx
import numpy as np
from ase import Atoms
from ase.formula import Formula as ASEFormula
from ase.utils import pbc2pbc
-from MDAnalysis.core._get_readers import get_reader_for
-from MDAnalysis.core.topology import Topology
-from MDAnalysis.core.universe import Universe
-from nptyping import Int, NDArray
-from pymatgen.core import Composition
-from pymatgen.core.periodic_table import get_el_sp
-from scipy import sparse
+from nptyping import NDArray
from scipy.spatial import Voronoi # pylint: disable=no-name-in-module
-from scipy.stats import linregress
from nomad.aflow_prototypes import aflow_prototypes
from nomad.constants import atomic_masses
-from nomad.metainfo import MSection
-from nomad.units import ureg
valid_elements = set(ase.data.chemical_symbols[1:])
@@ -944,6 +927,8 @@ class Formula:
# Try if can be interpreted as fractional formula
except Exception:
try:
+ from pymatgen.core import Composition
+
self.ase_formula = ASEFormula(
Composition(formula).get_integer_formula_and_factor()[0]
)
@@ -1150,6 +1135,8 @@ class Formula:
def _formula_iupac(self) -> str:
"""Returns the IUPAC formula."""
+ from pymatgen.core.periodic_table import get_el_sp
+
count = self.count()
counts = count.values()
symbols = list(count.keys())
@@ -1274,1129 +1261,3 @@ class Formula:
Chemical formula as a string.
"""
return ''.join(symb + (str(n) if n > 1 else '') for symb, n in dct.items())
-
-
-def create_empty_universe(
- n_atoms: int,
- n_frames: int = 1,
- n_residues: int = 1,
- n_segments: int = 1,
- atom_resindex: NDArray[Int] = None,
- residue_segindex: NDArray[Int] = None,
- flag_trajectory: bool = False,
- flag_velocities: bool = False,
- flag_forces: bool = False,
- timestep: float = None,
-) -> MDAnalysis.Universe:
- """Create a blank Universe
-
- This function was adapted from the function empty() within the MDA class Universe().
- The only difference is that the Universe() class is imported directly here, whereas in the
- original function is is passed as a function argument, since the function there is a classfunction.
-
- Useful for building a Universe without requiring existing files,
- for example for system building.
-
- If `flag_trajectory` is set to True, a
- :class:`MDAnalysis.coordinates.memory.MemoryReader` will be
- attached to the Universe.
-
- Parameters
- ----------
- n_atoms: int
- number of Atoms in the Universe
- n_residues: int, default 1
- number of Residues in the Universe, defaults to 1
- n_segments: int, default 1
- number of Segments in the Universe, defaults to 1
- atom_resindex: array like, optional
- mapping of atoms to residues, e.g. with 6 atoms,
- `atom_resindex=[0, 0, 1, 1, 2, 2]` would put 2 atoms
- into each of 3 residues.
- residue_segindex: array like, optional
- mapping of residues to segments
- flag_trajectory: bool, optional
- if True, attaches a :class:`MDAnalysis.coordinates.memory.MemoryReader`
- allowing coordinates to be set and written. Default is False
- flag_velocities: bool, optional
- include velocities in the :class:`MDAnalysis.coordinates.memory.MemoryReader`
- flag_forces: bool, optional
- include forces in the :class:`MDAnalysis.coordinates.memory.MemoryReader`
-
- Returns
- -------
- MDAnalysis.Universe object
-
- Examples
- --------
- For example to create a new Universe with 6 atoms in 2 residues, with
- positions for the atoms and a mass attribute:
-
- >>> u = mda.Universe.empty(6, 2,
- atom_resindex=np.array([0, 0, 0, 1, 1, 1]),
- flag_trajectory=True,
- )
- >>> u.add_TopologyAttr('masses')
-
- .. versionadded:: 0.17.0
- .. versionchanged:: 0.19.0
- The attached Reader when flag_trajectory=True is now a MemoryReader
- .. versionchanged:: 1.0.0
- Universes can now be created with 0 atoms
- """
-
- if not n_atoms:
- n_residues = 0
- n_segments = 0
-
- if atom_resindex is None:
- warnings.warn(
- 'Residues specified but no atom_resindex given. '
- 'All atoms will be placed in first Residue.',
- UserWarning,
- )
-
- if residue_segindex is None:
- warnings.warn(
- 'Segments specified but no segment_resindex given. '
- 'All residues will be placed in first Segment',
- UserWarning,
- )
-
- topology = Topology(
- n_atoms,
- n_residues,
- n_segments,
- atom_resindex=atom_resindex,
- residue_segindex=residue_segindex,
- )
-
- universe = Universe(topology)
-
- if flag_trajectory:
- coords = np.zeros((n_frames, n_atoms, 3), dtype=np.float32)
- vels = np.zeros_like(coords) if flag_velocities else None
- forces = np.zeros_like(coords) if flag_forces else None
-
- # grab and attach a MemoryReader
- universe.trajectory = get_reader_for(coords)(
- coords,
- order='fac',
- n_atoms=n_atoms,
- velocities=vels,
- forces=forces,
- dt=timestep,
- )
-
- return universe
-
-
-def archive_to_universe(
- archive,
- system_index: int = 0,
- method_index: int = -1,
- model_index: int = -1,
-) -> MDAnalysis.Universe:
- """Extract the topology from a provided run section of an archive entry
-
- Input:
-
- archive_sec_run: section run of an EntryArchive
-
- system_index: list index of archive.run[].system to be used for topology extraction
-
- method_index: list index of archive.run[].method to be used for atom parameter (charges and masses) extraction
-
- model_index: list index of archive.run[].method[].force_field.model for bond list extraction
-
- Variables:
-
- n_frames (int):
-
- n_atoms (int):
-
- atom_names (str, shape=(n_atoms)):
-
- atom_types (str, shape=(n_atoms)):
-
- atom_resindex (str, shape=(n_atoms)):
-
- atom_segids (str, shape=(n_atoms)):
-
- n_segments (int): Segments correspond to a group of the same type of molecules.
-
- n_residues (int): The number of distinct residues (nb - individual molecules are also denoted as a residue).
-
- resnames (str, shape=(n_residues)): The name of each residue.
-
- residue_segindex (int, shape=(n_residues)): The segment index that each residue belongs to.
-
- residue_molnums (int, shape=(n_residues)): The molecule index that each residue belongs to.
-
- residue_moltypes (int, shape=(n_residues)): The molecule type of each residue.
-
- n_molecules (int):
-
- masses (float, shape=(n_atoms)): atom masses, units = amu
-
- charges (float, shape=(n_atoms)): atom partial charges, units = e
-
- positions (float, shape=(n_frames,n_atoms,3)): atom positions
-
- velocities (float, shape=(n_frames,n_atoms,3)): atom velocities
-
- dimensions (float, shape=(n_frames,6)): box dimensions (nb - currently assuming a cubic box!)
-
- bonds (tuple, shape=([])): list of tuples with the atom indices of each bond
- """
-
- try:
- sec_run = archive.run[-1]
- sec_system = sec_run.system
- sec_system_top = sec_run.system[system_index]
- sec_atoms = sec_system_top.atoms
- sec_atoms_group = sec_system_top.atoms_group
- sec_calculation = sec_run.calculation
- sec_method = (
- sec_run.method[method_index] if sec_run.get('method') is not None else None
- )
- except IndexError:
- logging.warning(
- 'Supplied indices or necessary sections do not exist in archive. Cannot build the MDA universe.'
- )
- return None
-
- n_atoms = sec_atoms.get('n_atoms')
- if n_atoms is None:
- logging.warning('No atoms found in the archive. Cannot build the MDA universe.')
- return None
-
- n_frames = len(sec_system) if sec_system is not None else None
- atom_names = sec_atoms.get('labels')
- model_atom_parameters = sec_method.get('atom_parameters')
- atom_types = (
- [atom.label for atom in model_atom_parameters]
- if model_atom_parameters
- else atom_names
- )
- atom_resindex = np.arange(n_atoms)
- atoms_segindices = np.empty(n_atoms)
- atom_segids = np.array(range(n_atoms), dtype='object')
- molecule_groups = sec_atoms_group
- n_segments = len(molecule_groups)
-
- n_residues = 0
- n_molecules = 0
- residue_segindex = []
- resnames = []
- residue_moltypes = []
- residue_min_atom_index = []
- residue_n_atoms = []
- molecule_n_res = []
- for mol_group_ind, mol_group in enumerate(molecule_groups):
- atoms_segindices[mol_group.atom_indices] = mol_group_ind
- atom_segids[mol_group.atom_indices] = mol_group.label
- molecules = mol_group.atoms_group if mol_group.atoms_group is not None else []
- for mol in molecules:
- monomer_groups = mol.atoms_group
- mol_res_counter = 0
- if monomer_groups:
- for mon_group in monomer_groups:
- monomers = mon_group.atoms_group
- for mon in monomers:
- resnames.append(mon.label)
- residue_segindex.append(mol_group_ind)
- residue_moltypes.append(mol.label)
- residue_min_atom_index.append(np.min(mon.atom_indices))
- residue_n_atoms.append(len(mon.atom_indices))
- n_residues += 1
- mol_res_counter += 1
- else: # no monomers => whole molecule is it's own residue
- resnames.append(mol.label)
- residue_segindex.append(mol_group_ind)
- residue_moltypes.append(mol.label)
- residue_min_atom_index.append(np.min(mol.atom_indices))
- residue_n_atoms.append(len(mol.atom_indices))
- n_residues += 1
- mol_res_counter += 1
- molecule_n_res.append(mol_res_counter)
- n_molecules += 1
-
- # reorder the residues by atom_indices
- residue_data = np.array(
- [
- [
- residue_min_atom_index[i],
- residue_n_atoms[i],
- residue_segindex[i],
- residue_moltypes[i],
- resnames[i],
- ]
- for i in range(len(residue_min_atom_index))
- ],
- dtype=object,
- )
- residue_data = np.array(sorted(residue_data, key=lambda x: x[0], reverse=False)).T
- residue_n_atoms = residue_data[1].astype(int)
- residue_segindex = residue_data[2].astype(int)
- residue_moltypes = residue_data[3]
- resnames = residue_data[4]
- res_index_counter = 0
- for i_residue, res_n_atoms in enumerate(residue_n_atoms):
- atom_resindex[res_index_counter : res_index_counter + res_n_atoms] = i_residue # type: ignore
- res_index_counter += res_n_atoms
- residue_molnums = np.array(range(n_residues))
- mol_index_counter = 0
- for i_molecule, n_res in enumerate(molecule_n_res):
- residue_molnums[mol_index_counter : mol_index_counter + n_res] = i_molecule
- mol_index_counter += n_res
-
- # get the atom masses and charges
-
- masses = np.empty(n_atoms)
- charges = np.empty(n_atoms)
- atom_parameters = (
- sec_method.get('atom_parameters') if sec_method is not None else []
- )
- atom_parameters = atom_parameters if atom_parameters is not None else []
-
- for atom_ind, atom in enumerate(atom_parameters):
- if atom.get('mass'):
- masses[atom_ind] = ureg.convert(
- atom.mass.magnitude, atom.mass.units, ureg.amu
- )
- if atom.get('charge'):
- charges[atom_ind] = ureg.convert(
- atom.charge.magnitude, atom.charge.units, ureg.e
- )
-
- # get the atom positions, velocites, and box dimensions
- positions = np.empty(shape=(n_frames, n_atoms, 3))
- velocities = np.empty(shape=(n_frames, n_atoms, 3))
- dimensions = np.empty(shape=(n_frames, 6))
- for frame_ind, frame in enumerate(sec_system):
- sec_atoms_fr = frame.get('atoms')
- if sec_atoms_fr is not None:
- positions_frame = sec_atoms_fr.positions
- positions[frame_ind] = (
- ureg.convert(
- positions_frame.magnitude, positions_frame.units, ureg.angstrom
- )
- if positions_frame is not None
- else None
- )
- velocities_frame = sec_atoms_fr.velocities
- velocities[frame_ind] = (
- ureg.convert(
- velocities_frame.magnitude,
- velocities_frame.units,
- ureg.angstrom / ureg.picosecond,
- )
- if velocities_frame is not None
- else None
- )
- latt_vec_tmp = sec_atoms_fr.get('lattice_vectors')
- if latt_vec_tmp is not None:
- length_conversion = ureg.convert(
- 1.0, sec_atoms_fr.lattice_vectors.units, ureg.angstrom
- )
- dimensions[frame_ind] = [
- sec_atoms_fr.lattice_vectors.magnitude[0][0] * length_conversion,
- sec_atoms_fr.lattice_vectors.magnitude[1][1] * length_conversion,
- sec_atoms_fr.lattice_vectors.magnitude[2][2] * length_conversion,
- 90,
- 90,
- 90,
- ] # TODO: extend to non-cubic boxes
-
- # get the bonds # TODO extend to multiple storage options for interactions
- bonds = sec_atoms.bond_list
- if bonds is None:
- bonds = get_bond_list_from_model_contributions(
- sec_run, method_index=-1, model_index=-1
- )
-
- # get the system times
- system_timestep = 1.0 * ureg.picosecond
-
- def approx(a, b, rel_tol=1e-09, abs_tol=0.0):
- return abs(a - b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
-
- system_times = [calc.time for calc in sec_calculation if calc.system_ref]
- if system_times:
- try:
- method = archive.workflow2.method
- system_timestep = (
- method.integration_timestep * method.coordinate_save_frequency
- )
- except Exception:
- logging.warning(
- 'Cannot find the system times. MDA universe will contain non-physical times and timestep.'
- )
- else:
- time_steps = [
- system_times[i_time] - system_times[i_time - 1]
- for i_time in range(1, len(system_times))
- ]
- if all(approx(time_steps[0], time_step) for time_step in time_steps):
- system_timestep = ureg.convert(
- time_steps[0].magnitude, ureg.second, ureg.picosecond
- )
- else:
- logging.warning(
- 'System times are not equally spaced. Cannot set system times in MDA universe.'
- ' MDA universe will contain non-physical times and timestep.'
- )
-
- system_timestep = ureg.convert(
- system_timestep, system_timestep._units, ureg.picoseconds
- )
-
- # create the Universe
- metainfo_universe = create_empty_universe(
- n_atoms,
- n_frames=n_frames,
- n_residues=n_residues,
- n_segments=n_segments,
- atom_resindex=atom_resindex,
- residue_segindex=residue_segindex,
- flag_trajectory=True,
- flag_velocities=True,
- timestep=system_timestep.magnitude,
- )
-
- # set the positions and velocities
- for frame_ind, frame in enumerate(metainfo_universe.trajectory):
- metainfo_universe.atoms.positions = positions[frame_ind]
- metainfo_universe.atoms.velocities = velocities[frame_ind]
-
- # add the atom attributes
- metainfo_universe.add_TopologyAttr('name', atom_names)
- metainfo_universe.add_TopologyAttr('type', atom_types)
- metainfo_universe.add_TopologyAttr('mass', masses)
- metainfo_universe.add_TopologyAttr('charge', charges)
- if n_segments != 0:
- metainfo_universe.add_TopologyAttr('segids', np.unique(atom_segids))
- if n_residues != 0:
- metainfo_universe.add_TopologyAttr('resnames', resnames)
- metainfo_universe.add_TopologyAttr('resids', np.unique(atom_resindex) + 1)
- metainfo_universe.add_TopologyAttr('resnums', np.unique(atom_resindex) + 1)
- if len(residue_molnums) > 0:
- metainfo_universe.add_TopologyAttr('molnums', residue_molnums)
- if len(residue_moltypes) > 0:
- metainfo_universe.add_TopologyAttr('moltypes', residue_moltypes)
-
- # add the box dimensions
- for frame_ind, frame in enumerate(metainfo_universe.trajectory):
- metainfo_universe.atoms.dimensions = dimensions[frame_ind]
-
- # add the bonds
- if hasattr(metainfo_universe, 'bonds'):
- logging.warning('archive_to_universe() failed, universe already has bonds.')
- return None
- metainfo_universe.add_TopologyAttr('bonds', bonds)
-
- return metainfo_universe
-
-
-class BeadGroup(object):
- # see https://github.com/MDAnalysis/mdanalysis/issues/1891#issuecomment-387138110
- # by @richardjgowers with performance improvements
- def __init__(self, atoms, compound='fragments'):
- """Initialize with an AtomGroup instance.
- Will split based on keyword 'compounds' (residues or fragments).
- """
- self._atoms = atoms
- self.compound = compound
- self._nbeads = len(getattr(self._atoms, self.compound))
- # for caching
- self._cache = {}
- self._cache['positions'] = None
- self.__last_frame = None
-
- def __len__(self):
- return self._nbeads
-
- @property
- def positions(self):
- # cache positions for current frame
- if self.universe.trajectory.frame != self.__last_frame:
- self._cache['positions'] = self._atoms.center_of_mass(
- unwrap=True, compound=self.compound
- )
- self.__last_frame = self.universe.trajectory.frame
- return self._cache['positions']
-
- @property # type: ignore
- @MDAnalysis.lib.util.cached('universe')
- def universe(self):
- return self._atoms.universe
-
-
-def __log_indices(first: int, last: int, num: int = 100):
- ls = np.logspace(0, np.log10(last - first + 1), num=num)
- return np.unique(np.int_(ls) - 1 + first)
-
-
-def __correlation(function, positions: List[float]):
- iterator = iter(positions)
- start_frame = next(iterator)
- return map(lambda f: function(start_frame, f), chain([start_frame], iterator))
-
-
-def shifted_correlation_average(
- function: Callable,
- times: NDArray,
- positions: NDArray,
- index_distribution: Callable = __log_indices,
- correlation: Callable = __correlation,
- segments: int = 10,
- window: float = 0.5,
- skip: int = 0,
-) -> tuple[NDArray, NDArray]:
- """
- Code adapted from MDevaluate module: https://github.com/mdevaluate/mdevaluate.git
-
- Calculate the time series for a correlation function.
-
- The times at which the correlation is calculated are determined automatically by the
- function given as ``index_distribution``. The default is a logarithmic distribution.
-
- The function has been edited so that the average is always calculated, i.e., average=True below.
-
- Args:
- function: The function that should be correlated
- positions: The coordinates of the simulation data
- index_distribution (opt.):
- A function that returns the indices for which the timeseries
- will be calculated
- correlation (function, opt.):
- The correlation function
- segments (int, opt.):
- The number of segments the time window will be shifted
- window (float, opt.):
- The fraction of the simulation the time series will cover
- skip (float, opt.):
- The fraction of the trajectory that will be skipped at the beginning,
- if this is None the start index of the frames slice will be used,
- which defaults to 0.
- counter (bool, opt.):
- If True, returns length of frames (in general number of particles specified)
- average (bool, opt.):
- If True,
- Returns:
- tuple:
- A list of length N that contains the indices of the frames at which
- the time series was calculated and a numpy array of shape (segments, N)
- that holds the (non-avaraged) correlation data
-
- if has_counter == True: adds number of counts to output tupel.
- if average is returned it will be weighted.
-
- Example:
- Calculating the mean square displacement of a coordinates object named ``coords``:
-
- >>> indices, data = shifted_correlation(msd, coords)
- """
- if window + skip >= 1:
- warnings.warn(
- 'Invalid parameters for shifted_correlation(), ' 'resetting to defaults.',
- UserWarning,
- )
- window = 0.5
- skip = 0
-
- start_frames = np.unique(
- np.linspace(
- len(positions) * skip,
- len(positions) * (1 - window),
- num=segments,
- endpoint=False,
- dtype=int,
- )
- )
- num_frames = int(len(positions) * (window))
-
- idx = index_distribution(0, num_frames)
-
- def correlate(start_frame):
- shifted_idx = idx + start_frame
- return correlation(function, map(positions.__getitem__, shifted_idx))
-
- correlation_times = np.array([times[i] for i in idx]) - times[0]
-
- result: NDArray
- for i_start_frame, start_frame in enumerate(start_frames):
- if i_start_frame == 0:
- result = np.array(list(correlate(start_frame)))
- else:
- result += np.array(list(correlate(start_frame)))
- result = np.array(result)
- result = result / len(start_frames)
-
- return correlation_times, result
-
-
-def _calc_diffusion_constant(
- times: NDArray, values: NDArray, dim: int = 3
-) -> tuple[float, float]:
- """
- Determines the diffusion constant from a fit of the mean squared displacement
- vs. time according to the Einstein relation.
- """
- linear_model = linregress(times, values)
- slope = linear_model.slope
- error = linear_model.rvalue
- return slope * 1 / (2 * dim), error
-
-
-def _get_molecular_bead_groups(
- universe: MDAnalysis.Universe, moltypes: List[str] = None
-) -> Dict[str, BeadGroup]:
- """
- Creates bead groups based on the molecular types as defined by the MDAnalysis universe.
- """
- if moltypes is None:
- atoms_moltypes = getattr(universe.atoms, 'moltypes', [])
- moltypes = np.unique(atoms_moltypes)
- bead_groups = {}
- for moltype in moltypes:
- ags_by_moltype = universe.select_atoms('moltype ' + moltype)
- ags_by_moltype = ags_by_moltype[
- ags_by_moltype.masses > abs(1e-2)
- ] # remove any virtual/massless sites (needed for, e.g., 4-bead water models)
- bead_groups[moltype] = BeadGroup(ags_by_moltype, compound='fragments')
-
- return bead_groups
-
-
-def calc_molecular_rdf(
- universe: MDAnalysis.Universe,
- n_traj_split: int = 10,
- n_prune: int = 1,
- interval_indices=None,
- max_mols: int = 5000,
-) -> Dict:
- """
- Calculates the radial distribution functions between for each unique pair of
- molecule types as a function of their center of mass distance.
-
- interval_indices: 2D array specifying the groups of the n_traj_split intervals to be averaged
- max_mols: the maximum number of molecules per bead group for calculating the rdf, for efficiency purposes.
- """
- # TODO 5k default for max_mols was set after > 50k was giving problems. Should do further testing to see where the appropriate limit should be set.
- if (
- not universe
- or not universe.trajectory
- or universe.trajectory[0].dimensions is None
- ):
- return {}
-
- n_frames = universe.trajectory.n_frames
- if n_frames < n_traj_split:
- n_traj_split = 1
- frames_start = np.array([0])
- frames_end = np.array([n_frames])
- n_frames_split = np.array([n_frames])
- interval_indices = [[0]]
- else:
- run_len = int(n_frames / n_traj_split)
- frames_start = np.arange(n_traj_split) * run_len
- frames_end = frames_start + run_len
- frames_end[-1] = n_frames
- n_frames_split = frames_end - frames_start
- if np.sum(n_frames_split) != n_frames:
- logging.error(
- 'Something went wrong with input parameters in calc_molecular_rdf().'
- 'Radial distribution functions will not be calculated.'
- )
- return {}
- if not interval_indices:
- interval_indices = [[i] for i in range(n_traj_split)]
-
- bead_groups = _get_molecular_bead_groups(universe)
- if not bead_groups:
- return bead_groups
- moltypes = [moltype for moltype in bead_groups.keys()]
- del_list = [
- i_moltype
- for i_moltype, moltype in enumerate(moltypes)
- if bead_groups[moltype]._nbeads > max_mols
- ]
- moltypes = np.delete(moltypes, del_list).tolist()
-
- min_box_dimension = np.min(universe.trajectory[0].dimensions[:3])
- max_rdf_dist = min_box_dimension / 2
- n_bins = 200
- n_smooth = 2
-
- rdf_results: Dict[str, Any] = {}
- rdf_results['n_smooth'] = n_smooth
- rdf_results['n_prune'] = n_prune
- rdf_results['type'] = 'molecular'
- rdf_results['types'] = []
- rdf_results['variables_name'] = []
- rdf_results['bins'] = []
- rdf_results['value'] = []
- rdf_results['frame_start'] = []
- rdf_results['frame_end'] = []
- for i, moltype_i in enumerate(moltypes):
- for j, moltype_j in enumerate(moltypes):
- if j > i:
- continue
- elif (
- i == j and bead_groups[moltype_i].positions.shape[0] == 1
- ): # skip if only 1 mol in group
- continue
-
- if i == j:
- exclusion_block = (1, 1) # remove self-distance
- else:
- exclusion_block = None
- pair_type = f'{moltype_i}-{moltype_j}'
- rdf_results_interval: Dict[str, Any] = {}
- rdf_results_interval['types'] = []
- rdf_results_interval['variables_name'] = []
- rdf_results_interval['bins'] = []
- rdf_results_interval['value'] = []
- rdf_results_interval['frame_start'] = []
- rdf_results_interval['frame_end'] = []
- for i_interval in range(n_traj_split):
- rdf_results_interval['types'].append(pair_type)
- rdf_results_interval['variables_name'].append(['distance'])
- rdf = MDA_RDF.InterRDF(
- bead_groups[moltype_i],
- bead_groups[moltype_j],
- range=(0, max_rdf_dist),
- exclusion_block=exclusion_block,
- nbins=n_bins,
- ).run(frames_start[i_interval], frames_end[i_interval], n_prune)
- rdf_results_interval['frame_start'].append(frames_start[i_interval])
- rdf_results_interval['frame_end'].append(frames_end[i_interval])
-
- rdf_results_interval['bins'].append(
- rdf.results.bins[int(n_smooth / 2) : -int(n_smooth / 2)]
- * ureg.angstrom
- )
- rdf_results_interval['value'].append(
- np.convolve(
- rdf.results.rdf, np.ones((n_smooth,)) / n_smooth, mode='same'
- )[int(n_smooth / 2) : -int(n_smooth / 2)]
- )
-
- flag_logging_error = False
- for interval_group in interval_indices:
- split_weights = n_frames_split[np.array(interval_group)] / np.sum(
- n_frames_split[np.array(interval_group)]
- )
- if abs(np.sum(split_weights) - 1.0) > 1e-6:
- flag_logging_error = True
- continue
- rdf_values_avg = (
- split_weights[0] * rdf_results_interval['value'][interval_group[0]]
- )
- for i_interval, interval in enumerate(interval_group[1:]):
- if (
- rdf_results_interval['types'][interval]
- != rdf_results_interval['types'][interval - 1]
- ):
- flag_logging_error = True
- continue
- if (
- rdf_results_interval['variables_name'][interval]
- != rdf_results_interval['variables_name'][interval - 1]
- ):
- flag_logging_error = True
- continue
- if not (
- rdf_results_interval['bins'][interval]
- == rdf_results_interval['bins'][interval - 1]
- ).all():
- flag_logging_error = True
- continue
- rdf_values_avg += (
- split_weights[i_interval + 1]
- * rdf_results_interval['value'][interval]
- )
- if flag_logging_error:
- logging.error(
- 'Something went wrong in calc_molecular_rdf(). Some interval groups were skipped.'
- )
- rdf_results['types'].append(
- rdf_results_interval['types'][interval_group[0]]
- )
- rdf_results['variables_name'].append(
- rdf_results_interval['variables_name'][interval_group[0]]
- )
- rdf_results['bins'].append(
- rdf_results_interval['bins'][interval_group[0]]
- )
- rdf_results['value'].append(rdf_values_avg)
- rdf_results['frame_start'].append(
- int(rdf_results_interval['frame_start'][interval_group[0]])
- )
- rdf_results['frame_end'].append(
- int(rdf_results_interval['frame_end'][interval_group[-1]])
- )
-
- return rdf_results
-
-
-def calc_molecular_mean_squared_displacements(
- universe: MDAnalysis.Universe, max_mols: int = 5000
-) -> Dict:
- """
- Calculates the mean squared displacement for the center of mass of each
- molecule type.
-
- max_mols: the maximum number of molecules per bead group for calculating the msd, for efficiency purposes.
- 50k was tested and is very fast and does not seem to have any memory issues.
- """
-
- def parse_jumps(
- universe: MDAnalysis.Universe, selection: MDAnalysis.AtomGroup
- ): # TODO Add output declaration
- """
- See __get_nojump_positions().
- """
- __ = universe.trajectory[0]
- prev = np.array(selection.positions)
- box = universe.trajectory[0].dimensions[:3]
- sparse_data = namedtuple('SparseData', ['data', 'row', 'col']) # type: ignore[name-match]
- jump_data = (
- sparse_data(data=array('b'), row=array('l'), col=array('l')),
- sparse_data(data=array('b'), row=array('l'), col=array('l')),
- sparse_data(data=array('b'), row=array('l'), col=array('l')),
- )
-
- for i_frame, _ in enumerate(universe.trajectory[1:]):
- curr = np.array(selection.positions)
- delta = ((curr - prev) / box).round().astype(np.int8)
- prev = np.array(curr)
- for d in range(3):
- (col,) = np.where(delta[:, d] != 0)
- jump_data[d].col.extend(col)
- jump_data[d].row.extend([i_frame] * len(col))
- jump_data[d].data.extend(delta[col, d])
-
- return jump_data
-
- def generate_nojump_matrices(
- universe: MDAnalysis.Universe, selection: MDAnalysis.AtomGroup
- ): # TODO Add output declaration
- """
- See __get_nojump_positions().
- """
- jump_data = parse_jumps(universe, selection)
- n_frames = len(universe.trajectory)
- n_atoms = selection.positions.shape[0]
-
- nojump_matrices = tuple(
- sparse.csr_matrix(
- (np.array(m.data), (m.row, m.col)), shape=(n_frames, n_atoms)
- )
- for m in jump_data
- )
- return nojump_matrices
-
- def get_nojump_positions(
- universe: MDAnalysis.Universe, selection: MDAnalysis.AtomGroup
- ) -> NDArray:
- """
- Unwraps the positions to create a continuous trajectory without jumps across periodic boundaries.
- """
- nojump_matrices = generate_nojump_matrices(universe, selection)
- box = universe.trajectory[0].dimensions[:3]
-
- nojump_positions = []
- for i_frame, __ in enumerate(universe.trajectory):
- delta = (
- np.array(
- np.vstack([m[:i_frame, :].sum(axis=0) for m in nojump_matrices]).T
- )
- * box
- )
- nojump_positions.append(selection.positions - delta)
-
- return np.array(nojump_positions)
-
- def mean_squared_displacement(start: NDArray, current: NDArray):
- """
- Calculates mean square displacement between current and initial (start) coordinates.
- """
- vec = start - current
- return (vec**2).sum(axis=1).mean()
-
- if (
- not universe
- or not universe.trajectory
- or universe.trajectory[0].dimensions is None
- ):
- return {}
-
- n_frames = universe.trajectory.n_frames
- if n_frames < 50:
- warnings.warn(
- 'At least 50 frames required to calculate molecular'
- ' mean squared displacements, skipping.',
- UserWarning,
- )
- return {}
-
- dt = getattr(universe.trajectory, 'dt')
- if dt is None:
- warnings.warn(
- 'Universe is missing time step, cannot calculate molecular'
- ' mean squared displacements, skipping.',
- UserWarning,
- )
- return {}
- times = np.arange(n_frames) * dt
-
- bead_groups = _get_molecular_bead_groups(universe)
- if bead_groups is {}:
- return bead_groups
-
- moltypes = [moltype for moltype in bead_groups.keys()]
- del_list = []
- for i_moltype, moltype in enumerate(moltypes):
- if bead_groups[moltype]._nbeads > max_mols:
- if max_mols > 50000:
- warnings.warn(
- 'Calculating mean squared displacements for more than 50k molecules.'
- ' Expect long processing times!',
- UserWarning,
- )
- try:
- # select max_mols nr. of rnd molecules from this moltype
- moltype_indices = np.array(
- [atom._ix for atom in bead_groups[moltype]._atoms]
- )
- molnums = universe.atoms.molnums[moltype_indices]
- molnum_types = np.unique(molnums)
- molnum_types_rnd = np.sort(
- np.random.choice(molnum_types, size=max_mols)
- )
- atom_indices_rnd = np.concatenate(
- [np.where(molnums == molnum)[0] for molnum in molnum_types_rnd]
- )
- selection = ' '.join([str(i) for i in atom_indices_rnd])
- selection = f'index {selection}'
- ags_moltype_rnd = universe.select_atoms(selection)
- bead_groups[moltype] = BeadGroup(ags_moltype_rnd, compound='fragments')
- warnings.warn(
- 'Maximum number of molecules for calculating the msd has been reached.'
- ' Will make a random selection for calculation.'
- )
- except Exception:
- warnings.warn(
- 'Error in selecting random molecules for large group when calculating msd. Skipping this molecule type.'
- )
- del_list.append(i_moltype)
-
- for index in sorted(del_list, reverse=True):
- del moltypes[index]
-
- msd_results: Dict[str, Any] = {}
- msd_results['type'] = 'molecular'
- msd_results['direction'] = 'xyz'
- msd_results['value'] = []
- msd_results['times'] = []
- msd_results['diffusion_constant'] = []
- msd_results['error_diffusion_constant'] = []
- for moltype in moltypes:
- positions = get_nojump_positions(universe, bead_groups[moltype])
- results = shifted_correlation_average(
- mean_squared_displacement, times, positions
- )
- if results:
- msd_results['value'].append(results[1])
- msd_results['times'].append(results[0])
- diffusion_constant, error = _calc_diffusion_constant(*results)
- msd_results['diffusion_constant'].append(diffusion_constant)
- msd_results['error_diffusion_constant'].append(error)
-
- msd_results['types'] = moltypes
- msd_results['times'] = np.array(msd_results['times']) * ureg.picosecond
- msd_results['value'] = np.array(msd_results['value']) * ureg.angstrom**2
- msd_results['diffusion_constant'] = (
- np.array(msd_results['diffusion_constant']) * ureg.angstrom**2 / ureg.picosecond
- )
- msd_results['error_diffusion_constant'] = np.array(
- msd_results['error_diffusion_constant']
- )
-
- return msd_results
-
-
-def calc_radius_of_gyration(
- universe: MDAnalysis.Universe, molecule_atom_indices: NDArray
-) -> Dict:
- """
- Calculates the radius of gyration as a function of time for the atoms 'molecule_atom_indices'.
- """
- if (
- not universe
- or not universe.trajectory
- or universe.trajectory[0].dimensions is None
- ):
- return {}
- selection = ' '.join([str(i) for i in molecule_atom_indices])
- selection = f'index {selection}'
- molecule = universe.select_atoms(selection)
- rg_results: Dict[str, Any] = {}
- rg_results['type'] = 'molecular'
- rg_results['times'] = []
- rg_results['value'] = []
- time_unit = hasattr(universe.trajectory.time, 'units')
- for __ in universe.trajectory:
- rg_results['times'].append(
- universe.trajectory.time.magnitude
- if time_unit
- else universe.trajectory.time
- )
- rg_results['value'].append(molecule.radius_of_gyration())
- rg_results['n_frames'] = len(rg_results['times'])
- rg_results['times'] = (
- np.array(rg_results['times']) * time_unit
- if time_unit
- else np.array(rg_results['times'])
- )
- rg_results['value'] = np.array(rg_results['value']) * ureg.angstrom
-
- return rg_results
-
-
-def calc_molecular_radius_of_gyration(
- universe: MDAnalysis.Universe, system_topology: MSection
-) -> List[Dict]:
- """
- Calculates the radius of gyration as a function of time for each polymer in the system.
- """
- if not system_topology:
- return []
-
- rg_results = []
- for molgroup in system_topology:
- for molecule in molgroup.get('atoms_group'):
- sec_monomer_groups = molecule.get('atoms_group')
- group_type = sec_monomer_groups[0].type if sec_monomer_groups else None
- if group_type != 'monomer_group':
- continue
- rg_result = calc_radius_of_gyration(universe, molecule.atom_indices)
- rg_result['label'] = molecule.label + '-index_' + str(molecule.index)
- rg_result['atomsgroup_ref'] = molecule
- rg_results.append(rg_result)
-
- return rg_results
-
-
-def get_molecules_from_bond_list(
- n_particles: int,
- bond_list: List[tuple],
- particle_types: List[str] = None,
- particles_typeid: array = None,
-) -> List[Dict]:
- """
- Returns a list of dictionaries with molecule info from each instance in the list of bonds.
- """
- system_graph = networkx.empty_graph(n_particles)
- system_graph.add_edges_from([(i[0], i[1]) for i in bond_list])
- molecules = [
- system_graph.subgraph(c).copy()
- for c in networkx.connected_components(system_graph)
- ]
- molecule_info: List[Dict] = []
- molecule_dict: Dict = {}
- for mol in molecules:
- molecule_dict = {}
- molecule_dict['indices'] = np.array(mol.nodes())
- molecule_dict['bonds'] = np.array(mol.edges())
- molecule_dict['type'] = 'molecule'
- molecule_dict['is_molecule'] = True
- if particles_typeid is None and len(particle_types) == n_particles:
- molecule_dict['names'] = [
- particle_types[int(x)]
- for x in sorted(np.array(molecule_dict['indices']))
- ]
- if particle_types is not None and particles_typeid is not None:
- molecule_dict['names'] = [
- particle_types[particles_typeid[int(x)]]
- for x in sorted(np.array(molecule_dict['indices']))
- ]
- molecule_info.append(molecule_dict)
- return molecule_info
-
-
-def is_same_molecule(mol_1: dict, mol_2: dict) -> bool:
- """
- Checks whether the 2 input molecule dictionary (see "get_molecules_from_bond_list()" above)
- represent the same molecule type, i.e., same particle types and corresponding bond connections.
- """
-
- def get_bond_list_dict(mol):
- mol_shift = np.min(mol['indices'])
- mol_bonds_shift = mol['bonds'] - mol_shift
- bond_list = [
- sorted((mol['names'][i], mol['names'][j])) for i, j in mol_bonds_shift
- ]
- bond_list_names, bond_list_counts = np.unique(
- bond_list, axis=0, return_counts=True
- )
-
- return {
- bond[0] + '-' + bond[1]: bond_list_counts[i_bond]
- for i_bond, bond in enumerate(bond_list_names)
- }
-
- if sorted(mol_1['names']) != sorted(mol_2['names']):
- return False
-
- bond_list_dict_1 = get_bond_list_dict(mol_1)
- bond_list_dict_2 = get_bond_list_dict(mol_2)
-
- if bond_list_dict_1 == bond_list_dict_2:
- return True
-
- return False
-
-
-def get_composition(children_names: List[str]) -> str:
- """
- Generates a generalized "chemical formula" based on the provided list `children_names`,
- with the format X(m)Y(n) for children_names X and Y of quantities m and n, respectively.
- """
- children_count_tup = np.unique(children_names, return_counts=True)
- formula = ''.join([f'{name}({count})' for name, count in zip(*children_count_tup)])
- return formula
-
-
-def get_bond_list_from_model_contributions(
- sec_run: MSection, method_index: int = -1, model_index: int = -1
-) -> List[tuple]:
- """
- Generates bond list of tuples using the list of bonded force field interactions stored under run[].method[].force_field.model[].
-
- bond_list: List[tuple]
- """
- contributions = []
- if sec_run.m_xpath(
- f'method[{method_index}].force_field.model[{model_index}].contributions'
- ):
- contributions = (
- sec_run.method[method_index].force_field.model[model_index].contributions
- )
- bond_list = []
- for contribution in contributions:
- if contribution.type != 'bond':
- continue
-
- atom_indices = contribution.atom_indices
- if (
- contribution.n_interactions
- ): # all bonds have been grouped into one contribution
- bond_list = [tuple(indices) for indices in atom_indices]
- else:
- bond_list.append(tuple(contribution.atom_indices))
-
- return bond_list
diff --git a/nomad/datamodel/metainfo/simulation/workflow.py b/nomad/datamodel/metainfo/simulation/workflow.py
index 8d9f2e172623c956f7d32e7d72bf59788cc038d5..a53db33ecc43112b05ad8fe2fbcce57ee243b732 100644
--- a/nomad/datamodel/metainfo/simulation/workflow.py
+++ b/nomad/datamodel/metainfo/simulation/workflow.py
@@ -66,12 +66,6 @@ from nomad.datamodel.metainfo.simulation.calculation import (
RadiusOfGyrationValues as RadiusOfGyrationValuesCalculation,
EnergyEntry,
)
-from nomad.atomutils import archive_to_universe
-from nomad.atomutils import (
- calc_molecular_rdf,
- calc_molecular_mean_squared_displacements,
- calc_molecular_radius_of_gyration,
-)
# TODO remove this after reprocessing with the new schema defined in
@@ -2208,7 +2202,18 @@ class MolecularDynamicsResults(ThermodynamicsResults):
def normalize(self, archive, logger):
super().normalize(archive, logger)
- universe = archive_to_universe(archive)
+ try:
+ from simulationworkflowschema.molecular_dynamics import archive_to_universe
+ from simulationworkflowschema.molecular_dynamics import (
+ calc_molecular_rdf,
+ calc_molecular_mean_squared_displacements,
+ calc_molecular_radius_of_gyration,
+ )
+
+ universe = archive_to_universe(archive)
+ except Exception:
+ universe = None
+
if universe is None:
return
diff --git a/nomad/normalizing/common.py b/nomad/normalizing/common.py
index 60c2e62696919ccd65b01386b4427dc951a6f45c..7f85a845aeab5a1937e80d9af0fddb55e52ccda7 100644
--- a/nomad/normalizing/common.py
+++ b/nomad/normalizing/common.py
@@ -20,7 +20,6 @@ from math import isnan
from ase import Atoms
from typing import List, Set, Any, Optional, Dict, Union
from nptyping import NDArray
-import MDAnalysis as mda
from matid import SymmetryAnalyzer # pylint: disable=import-error
from matid.symmetry.wyckoffset import WyckoffSet as WyckoffSetMatID # pylint: disable=import-error
import matid.geometry # pylint: disable=import-error
@@ -273,46 +272,6 @@ def ase_atoms_from_structure(system: Structure) -> Atoms:
)
-def mda_universe_from_nomad_atoms(system: Atoms, logger=None) -> mda.Universe:
- """Returns an instance of mda.Universe from a NOMAD Atoms-section.
-
- Args:
- system: The atoms to transform
-
- Returns:
- A new mda.Universe created from the given data.
- """
- n_atoms = len(system.positions)
- n_residues = 1
- atom_resindex = [0] * n_atoms
- residue_segindex = [0]
-
- universe = mda.Universe.empty(
- n_atoms,
- n_residues=n_residues,
- atom_resindex=atom_resindex,
- residue_segindex=residue_segindex,
- trajectory=True,
- )
-
- # Add positions
- universe.atoms.positions = system.positions.to(ureg.angstrom).magnitude
-
- # Add atom attributes
- atom_names = system.labels
- universe.add_TopologyAttr('name', atom_names)
- universe.add_TopologyAttr('type', atom_names)
- universe.add_TopologyAttr('element', atom_names)
-
- # Add the box dimensions
- if system.lattice_vectors is not None:
- universe.atoms.dimensions = atomutils.cell_to_cellpar(
- system.lattice_vectors.to(ureg.angstrom).magnitude, degrees=True
- )
-
- return universe
-
-
def structures_2d(original_atoms, logger=None):
conv_atoms = None
prim_atoms = None
diff --git a/pyproject.toml b/pyproject.toml
index 28fe31cf809d4ab2801b977022ed6f607dd155e6..e371a58c268f02b9efc1d20ed7eb35b0ba29c085 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,8 +29,6 @@ dependencies = [
'lxml>=5.2',
'lxml-html-clean>=0.1.0',
'matid>=2.1.2',
- 'mdanalysis==2.7.0',
- 'networkx>=2.6.3',
'nptyping~=1.4.4',
'numpy>=1.22.4,<2.0.0',
'openpyxl>=3.0.0',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index c5effa20ce226adcc984cd78be40d51d8304015b..30a9c097c109beaefd5b7cc22dad291f6c72505a 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -22,12 +22,12 @@ basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
billiard==4.2.0 # via celery, -r requirements.txt
bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-build==1.2.1 # via nomad-lab (pyproject.toml)
+build==1.2.2 # via nomad-lab (pyproject.toml)
cachetools==5.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt
certipy==0.1.3 # via jupyterhub, -r requirements.txt
-cffi==1.17.0 ; platform_python_implementation != 'PyPy' # via cryptography, -r requirements.txt
+cffi==1.17.1 ; platform_python_implementation != 'PyPy' # via cryptography, -r requirements.txt
cftime==1.6.4 # via netcdf4, -r requirements.txt
charset-normalizer==3.3.2 # via requests, -r requirements.txt
click==8.1.7 # via celery, click-didyoumean, click-plugins, click-repl, mkdocs, mkdocs-click, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml)
@@ -57,7 +57,6 @@ et-xmlfile==1.1.0 # via openpyxl, -r requirements.txt
execnet==2.1.1 # via pytest-xdist
executing==2.1.0 # via devtools
fastapi==0.99.1 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
-fasteners==0.19 # via mdanalysis, -r requirements.txt
filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
fonttools==4.53.1 # via matplotlib, -r requirements.txt
fqdn==1.5.1 # via jsonschema, -r requirements.txt
@@ -65,7 +64,6 @@ ghp-import==2.1.0 # via mkdocs
gitdb==4.0.11 # via gitpython, -r requirements.txt
gitpython==3.1.43 # via mkdocs-git-revision-date-localized-plugin, -r requirements.txt, nomad-lab (pyproject.toml)
greenlet==3.0.3 ; (python_full_version < '3.13' and platform_machine == 'AMD64') or (python_full_version < '3.13' and platform_machine == 'WIN32') or (python_full_version < '3.13' and platform_machine == 'aarch64') or (python_full_version < '3.13' and platform_machine == 'amd64') or (python_full_version < '3.13' and platform_machine == 'ppc64le') or (python_full_version < '3.13' and platform_machine == 'win32') or (python_full_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy, -r requirements.txt
-griddataformats==1.0.2 # via mdanalysis, -r requirements.txt
gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
h11==0.14.0 # via httpcore, uvicorn, -r requirements.txt
h5grove==1.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -89,7 +87,7 @@ jaraco-functools==4.0.2 # via keyring
jeepney==0.8.0 ; sys_platform == 'linux' # via keyring, secretstorage
jinja2==3.1.4 # via jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx, -r requirements.txt
jmespath==1.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn, -r requirements.txt
+joblib==1.4.2 # via pymatgen, scikit-learn, -r requirements.txt
jsonpointer==3.0.0 # via jsonschema, -r requirements.txt
jsonschema==4.17.3 # via jupyter-telemetry, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml)
jupyter-telemetry==0.1.0 # via jupyterhub, -r requirements.txt
@@ -108,43 +106,40 @@ mako==1.3.5 # via alembic, -r requirements.txt
markdown==3.7 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
markupsafe==2.1.5 # via jinja2, mako, mkdocs, -r requirements.txt, nomad-lab (pyproject.toml)
matid==2.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-matplotlib==3.9.2 # via ase, mdanalysis, pymatgen, -r requirements.txt
-mda-xdrlib==0.2.0 # via mdanalysis, pyedr, -r requirements.txt
-mdanalysis==2.7.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+matplotlib==3.9.2 # via ase, pymatgen, -r requirements.txt
+mda-xdrlib==0.2.0 # via pyedr, -r requirements.txt
mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps
mistune==3.0.2 # via m2r, -r requirements.txt
mkdocs==1.6.1 # via mkdocs-git-revision-date-localized-plugin, mkdocs-macros-plugin, mkdocs-material, mkdocs-redirects, nomad-lab (pyproject.toml)
mkdocs-click==0.8.1 # via nomad-lab (pyproject.toml)
mkdocs-get-deps==0.2.0 # via mkdocs
-mkdocs-git-revision-date-localized-plugin==1.2.7 # via nomad-lab (pyproject.toml)
+mkdocs-git-revision-date-localized-plugin==1.2.8 # via nomad-lab (pyproject.toml)
mkdocs-glightbox==0.4.0 # via nomad-lab (pyproject.toml)
mkdocs-macros-plugin==1.0.5 # via nomad-lab (pyproject.toml)
mkdocs-material==9.5.34 # via nomad-lab (pyproject.toml)
mkdocs-material-extensions==1.3.1 # via mkdocs-material, nomad-lab (pyproject.toml)
mkdocs-redirects==1.2.1 # via nomad-lab (pyproject.toml)
-mmtf-python==1.1.3 # via mdanalysis, -r requirements.txt
mongoengine==0.29.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade, -r requirements.txt
monty==2024.7.30 # via pymatgen, -r requirements.txt
-more-itertools==10.4.0 # via jaraco-classes, jaraco-functools
+more-itertools==10.5.0 # via jaraco-classes, jaraco-functools
mpmath==1.3.0 # via sympy, -r requirements.txt
-mrcfile==1.5.3 # via griddataformats, -r requirements.txt
-msgpack==1.0.8 # via mmtf-python, -r requirements.txt, nomad-lab (pyproject.toml)
+msgpack==1.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
mypy==1.0.1 # via nomad-lab (pyproject.toml)
mypy-extensions==1.0.0 # via mypy
names==0.3.0 # via nomad-lab (pyproject.toml)
netcdf4==1.6.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-networkx==3.3 # via matid, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
+networkx==3.3 # via matid, pymatgen, -r requirements.txt
nh3==0.2.18 # via readme-renderer
nomad-openbis==1.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-numpy==1.26.4 # via ase, cftime, contourpy, griddataformats, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
+numpy==1.26.4 # via ase, cftime, contourpy, h5grove, h5py, matid, matplotlib, netcdf4, nptyping, pandas, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub, -r requirements.txt
openpyxl==3.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
optimade==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
orjson==3.10.7 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
-packaging==24.1 # via build, deprecation, gunicorn, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt
+packaging==24.1 # via build, deprecation, gunicorn, jupyterhub, matplotlib, mkdocs, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt
paginate==0.5.7 # via mkdocs-material
palettable==3.3.3 # via pymatgen, -r requirements.txt
pamela==1.2.0 ; sys_platform != 'win32' # via jupyterhub, -r requirements.txt
@@ -155,7 +150,7 @@ pathspec==0.12.1 # via mkdocs
pillow==10.4.0 # via matplotlib, rdkit, -r requirements.txt
pint==0.17 # via -r requirements.txt, nomad-lab (pyproject.toml)
pkginfo==1.11.1 # via twine
-platformdirs==4.2.2 # via mkdocs-get-deps
+platformdirs==4.3.2 # via mkdocs-get-deps
plotly==5.24.0 # via pymatgen, -r requirements.txt
pluggy==1.5.0 # via pytest
prometheus-client==0.20.0 # via jupyterhub, -r requirements.txt
@@ -211,10 +206,10 @@ rfc3987==1.3.8 # via jsonschema, -r requirements.txt
rope==0.21.0 # via nomad-lab (pyproject.toml)
ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt
-ruff==0.6.3 # via nomad-lab (pyproject.toml)
+ruff==0.6.4 # via nomad-lab (pyproject.toml)
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-learn==1.5.1 # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
-scipy==1.14.1 # via ase, griddataformats, mdanalysis, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
+scipy==1.14.1 # via ase, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
secretstorage==3.3.3 ; sys_platform == 'linux' # via keyring
sentinels==1.0.0 # via mongomock, -r requirements.txt
six==1.16.0 # via asttokens, basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt
@@ -238,16 +233,16 @@ tabulate==0.8.9 # via nomad-openbis, pymatgen, -r requirements.txt, no
tenacity==9.0.0 # via plotly, -r requirements.txt
termcolor==2.4.0 # via mkdocs-macros-plugin
texttable==1.7.0 # via nomad-openbis, -r requirements.txt
-threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -r requirements.txt
+threadpoolctl==3.5.0 # via scikit-learn, -r requirements.txt
tifffile==2024.8.30 # via h5grove, -r requirements.txt
-tomli==2.0.1 ; python_full_version == '3.11' # via coverage
+tomli==2.0.1 ; python_full_version <= '3.11' # via coverage
toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml)
tornado==6.4.1 # via jupyterhub, -r requirements.txt
-tqdm==4.66.5 # via mdanalysis, pyedr, pymatgen, twine, -r requirements.txt
+tqdm==4.66.5 # via pyedr, pymatgen, twine, -r requirements.txt
traitlets==5.14.3 # via jupyter-telemetry, jupyterhub, -r requirements.txt
twine==3.4.2 # via nomad-lab (pyproject.toml)
typed-ast==1.5.5 # via nomad-lab (pyproject.toml)
-types-python-dateutil==2.9.0.20240821 # via arrow, -r requirements.txt
+types-python-dateutil==2.9.0.20240906 # via arrow, -r requirements.txt
typing-extensions==4.12.2 # via alembic, fastapi, jwcrypto, mypy, pydantic, sqlalchemy, -r requirements.txt
typish==1.9.3 # via nptyping, -r requirements.txt
tzdata==2024.1 # via celery, pandas, -r requirements.txt
@@ -255,7 +250,7 @@ uncertainties==3.2.2 # via pymatgen, -r requirements.txt
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema, -r requirements.txt
urllib3==1.26.20 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt
-uv==0.4.4 # via nomad-lab (pyproject.toml)
+uv==0.4.8 # via nomad-lab (pyproject.toml)
uvicorn==0.30.6 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
uvloop==0.20.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn, -r requirements.txt
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
diff --git a/requirements-plugins.txt b/requirements-plugins.txt
index 3b54d480d53d1df6c21e14bee3a8b4a0a0da5918..aaed4c6dabc56b77ae2c657898e95fdbe47455df 100644
--- a/requirements-plugins.txt
+++ b/requirements-plugins.txt
@@ -14,7 +14,7 @@ asteval==1.0.2 # via lmfit
asttokens==2.4.1 # via stack-data, -c requirements-dev.txt
async-lru==2.0.4 # via jupyterlab
async-property==0.2.2 # via python-keycloak, -c requirements-dev.txt
-atomisticparsers @ git+https://github.com/nomad-coe/atomistic-parsers.git@cedaf4191abe315001f6b55a9690dcd21116e9b7 # via -r default_plugins.txt
+atomisticparsers @ git+https://github.com/nomad-coe/atomistic-parsers.git@eebca28ebe83b3c945e922910b18a16ec36e8122 # via -r default_plugins.txt
attrs==24.2.0 # via jsonschema, -c requirements-dev.txt
babel==2.16.0 # via jupyterlab-server, -c requirements-dev.txt
beautifulsoup4==4.12.3 # via nbconvert, -c requirements-dev.txt
@@ -24,7 +24,8 @@ blinker==1.8.2 # via flask
blosc2==2.7.1 # via tables
cachetools==5.5.0 # via nomad-lab, -c requirements-dev.txt
certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -c requirements-dev.txt
-cffi==1.17.0 # via argon2-cffi-bindings, cryptography, pyzmq, -c requirements-dev.txt
+cffi==1.17.0 ; platform_python_implementation == 'PyPy' # via argon2-cffi-bindings, pyzmq, -c requirements-dev.txt
+cffi==1.17.1 ; platform_python_implementation != 'PyPy' # via argon2-cffi-bindings, cryptography, pyzmq, -c requirements-dev.txt
cftime==1.6.4 # via netcdf4, -c requirements-dev.txt
charset-normalizer==3.3.2 # via requests, -c requirements-dev.txt
click==8.1.7 # via asr, click-default-group, dask, flask, nomad-lab, pynxtools, -c requirements-dev.txt
@@ -48,13 +49,13 @@ docstring-parser==0.16 # via nomad-lab, -c requirements-dev.txt
eelsdbconverter @ git+https://github.com/nomad-coe/nomad-parser-eelsdb.git@788eb03dc71ef9b164e2a5ccb9c0209b546f5c38 # via -r default_plugins.txt
elasticsearch==7.17.1 # via elasticsearch-dsl, -c requirements-dev.txt
elasticsearch-dsl==7.4.0 # via nomad-lab, -c requirements-dev.txt
-electronicparsers @ git+https://github.com/nomad-coe/electronic-parsers.git@637a5d67fe84f8e4f1b18fdb2dd2df7ba199d1a9 # via -r default_plugins.txt
+electronicparsers @ git+https://github.com/nomad-coe/electronic-parsers.git@8d4ba60e1893afad1ad43df1bf0a0911f17bffc0 # via -r default_plugins.txt
entrypoints==0.4 # via ipyparallel
et-xmlfile==1.1.0 # via openpyxl, -c requirements-dev.txt
executing==2.1.0 # via stack-data, -c requirements-dev.txt
fabio==2024.4.0 # via pyfai, silx
fairmat-readers-xrd==0.0.6 # via pynxtools-xrd
-fasteners==0.19 # via mdanalysis, zarr, -c requirements-dev.txt
+fasteners==0.19 # via mdanalysis, zarr
fastjsonschema==2.20.0 # via nbformat
findiff==0.10.0 # via pynxtools-stm
flask==3.0.3 # via asr
@@ -63,7 +64,7 @@ fonttools==4.53.1 # via matplotlib, -c requirements-dev.txt
fqdn==1.5.1 # via jsonschema, -c requirements-dev.txt
fsspec==2024.6.1 # via dask, hyperspy
greenlet==3.0.3 ; (python_full_version < '3.13' and platform_machine == 'AMD64') or (python_full_version < '3.13' and platform_machine == 'WIN32') or (python_full_version < '3.13' and platform_machine == 'aarch64') or (python_full_version < '3.13' and platform_machine == 'amd64') or (python_full_version < '3.13' and platform_machine == 'ppc64le') or (python_full_version < '3.13' and platform_machine == 'win32') or (python_full_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy, -c requirements-dev.txt
-griddataformats==1.0.2 # via mdanalysis, -c requirements-dev.txt
+griddataformats==1.0.2 # via mdanalysis
h11==0.14.0 # via httpcore, -c requirements-dev.txt
h5grove==1.3.0 # via jupyterlab-h5web, -c requirements-dev.txt
h5py==3.11.0 # via electronicparsers, fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, kikuchipy, nionswift, nomad-lab, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, silx, workflowparsers, -c requirements-dev.txt
@@ -120,14 +121,14 @@ matplotlib==3.9.2 # via ase, asr, diffsims, hyperspy, kikuchipy, matplot
matplotlib-inline==0.1.7 # via ipykernel, ipython
matplotlib-scalebar==0.8.1 # via orix
mda-xdrlib==0.2.0 # via mdanalysis, pyedr, -c requirements-dev.txt
-mdanalysis==2.7.0 # via atomisticparsers, nomad-lab, -c requirements-dev.txt
+mdanalysis==2.7.0 # via atomisticparsers, nomad-lab, nomad-schema-plugin-simulation-workflow
mergedeep==1.3.4 # via pynxtools, -c requirements-dev.txt
mistune==3.0.2 # via nbconvert, -c requirements-dev.txt
-mmtf-python==1.1.3 # via mdanalysis, -c requirements-dev.txt
+mmtf-python==1.1.3 # via mdanalysis
monty==2024.7.30 # via pymatgen, -c requirements-dev.txt
mpmath==1.3.0 # via sympy, -c requirements-dev.txt
-mrcfile==1.5.3 # via griddataformats, -c requirements-dev.txt
-msgpack==1.0.8 # via blosc2, mmtf-python, -c requirements-dev.txt
+mrcfile==1.5.3 # via griddataformats
+msgpack==1.1.0 # via blosc2, mmtf-python, -c requirements-dev.txt
natsort==8.4.0 # via hyperspy
nbclient==0.10.0 # via nbconvert
nbconvert==7.16.4 # via jupyter, jupyter-server
@@ -135,7 +136,7 @@ nbformat==5.10.4 # via jupyter-server, nbclient, nbconvert
ndindex==1.8 # via blosc2
nest-asyncio==1.6.0 # via ipykernel
netcdf4==1.6.5 # via electronicparsers, -c requirements-dev.txt
-networkx==3.3 # via matid, nomad-lab, pymatgen, radioactivedecay, scikit-image, -c requirements-dev.txt
+networkx==3.3 # via matid, nomad-lab, nomad-schema-plugin-simulation-workflow, pymatgen, radioactivedecay, scikit-image, -c requirements-dev.txt
niondata==15.6.3 # via nionswift, nionswift-io
nionswift==16.11.0 # via pynxtools-em
nionswift-io==15.2.1 # via nionswift
@@ -151,7 +152,7 @@ nomad-normalizer-plugin-spectra @ git+https://github.com/nomad-coe/nomad-normali
nomad-normalizer-plugin-system @ git+https://github.com/nomad-coe/nomad-normalizer-plugin-system.git@01523ddbc85676a40af40f4747f5f13676f34c0f # via -r default_plugins.txt
nomad-porous-materials @ git+https://github.com/FAIRmat-NFDI/nomad-porous-materials.git@522f4a3208077f534f1c5e886527ee2104283d0b # via -r default_plugins.txt
nomad-schema-plugin-run @ git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@92d120dc4c5f7f4bcd94990ed009f8ac0019acec # via atomisticparsers, databaseparsers, electronicparsers, nomad-schema-plugin-simulation-workflow, simulationparsers, workflowparsers, -r default_plugins.txt
-nomad-schema-plugin-simulation-workflow @ git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@c9bd20c0447aaf22a6477cb39bdf03dea4c597f8 # via atomisticparsers, databaseparsers, electronicparsers, nomad-normalizer-plugin-simulation-workflow, workflowparsers, -r default_plugins.txt
+nomad-schema-plugin-simulation-workflow @ git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@5631278b983072a6e7cb6fea40c4b3ca49b7b804 # via atomisticparsers, databaseparsers, electronicparsers, nomad-normalizer-plugin-simulation-workflow, workflowparsers, -r default_plugins.txt
nomad-simulations==0.0.1 # via -r default_plugins.txt
notebook==7.1.3 # via jupyter
notebook-shim==0.2.4 # via jupyterlab, notebook
@@ -177,7 +178,7 @@ pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via
phonopy==2.11.0 # via asr, workflowparsers
pillow==10.4.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image, -c requirements-dev.txt
pint==0.17 # via fairmat-readers-xrd, hyperspy, nomad-lab, pynxtools-xps, pynxtools-xrd, rosettasciio, -c requirements-dev.txt
-platformdirs==4.2.2 # via jupyter-core, pooch, xraydb, -c requirements-dev.txt
+platformdirs==4.3.2 # via jupyter-core, pooch, xraydb, -c requirements-dev.txt
plotly==5.24.0 # via asr, pymatgen, -c requirements-dev.txt
pooch==1.8.2 # via kikuchipy, orix
prettytable==3.11.0 # via hyperspy
@@ -233,7 +234,7 @@ ruamel-yaml==0.18.6 # via pymatgen, -c requirements-dev.txt
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -c requirements-dev.txt
scikit-image==0.22.0 # via hyperspy, kikuchipy, pyxem
scikit-learn==1.5.1 # via kikuchipy, matid, nomad-lab, pyxem, -c requirements-dev.txt
-scipy==1.14.1 # via ase, atomisticparsers, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, mdanalysis, niondata, nionswift, nomad-lab, orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb, -c requirements-dev.txt
+scipy==1.14.1 # via ase, atomisticparsers, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, mdanalysis, niondata, nionswift, nomad-lab, nomad-schema-plugin-simulation-workflow, orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb, -c requirements-dev.txt
send2trash==1.8.3 # via jupyter-server
setuptools==73.0.1 # via pynxtools-xps, radioactivedecay
silx==2.1.1 # via pyfai
@@ -260,7 +261,7 @@ tqdm==4.66.5 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdan
traitlets==5.14.3 # via comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-console, jupyter-core, jupyter-events, jupyter-server, jupyterlab, matplotlib-inline, nbclient, nbconvert, nbformat, qtconsole, -c requirements-dev.txt
traits==6.4.3 # via hyperspy, pyxem
transforms3d==0.4.2 # via diffsims, pyxem
-types-python-dateutil==2.9.0.20240821 # via arrow, -c requirements-dev.txt
+types-python-dateutil==2.9.0.20240906 # via arrow, -c requirements-dev.txt
typing-extensions==4.12.2 # via ipython, jwcrypto, pydantic, sqlalchemy, tables, -c requirements-dev.txt
typish==1.9.3 # via nptyping, -c requirements-dev.txt
tzdata==2024.1 # via pandas, tzlocal, -c requirements-dev.txt
diff --git a/requirements.txt b/requirements.txt
index 49a969c73627e8b2777802781340c7a3a9e1127b..54ecbb99060d235c7569b45d1fcebe9dc9a6467f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -21,7 +21,7 @@ cachetools==5.5.0 # via nomad-lab (pyproject.toml)
celery==5.4.0 # via nomad-lab (pyproject.toml)
certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests
certipy==0.1.3 # via jupyterhub
-cffi==1.17.0 ; platform_python_implementation != 'PyPy' # via cryptography
+cffi==1.17.1 ; platform_python_implementation != 'PyPy' # via cryptography
cftime==1.6.4 # via netcdf4
charset-normalizer==3.3.2 # via requests
click==8.1.7 # via celery, click-didyoumean, click-plugins, click-repl, uvicorn, nomad-lab (pyproject.toml)
@@ -46,14 +46,12 @@ email-validator==1.3.1 # via optimade
escapism==1.0.1 # via dockerspawner
et-xmlfile==1.1.0 # via openpyxl
fastapi==0.99.1 # via h5grove, nomad-lab (pyproject.toml)
-fasteners==0.19 # via mdanalysis
filelock==3.3.1 # via nomad-lab (pyproject.toml)
fonttools==4.53.1 # via matplotlib
fqdn==1.5.1 # via jsonschema
gitdb==4.0.11 # via gitpython
gitpython==3.1.43 # via nomad-lab (pyproject.toml)
greenlet==3.0.3 ; (python_full_version < '3.13' and platform_machine == 'AMD64') or (python_full_version < '3.13' and platform_machine == 'WIN32') or (python_full_version < '3.13' and platform_machine == 'aarch64') or (python_full_version < '3.13' and platform_machine == 'amd64') or (python_full_version < '3.13' and platform_machine == 'ppc64le') or (python_full_version < '3.13' and platform_machine == 'win32') or (python_full_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy
-griddataformats==1.0.2 # via mdanalysis
gunicorn==21.2.0 # via nomad-lab (pyproject.toml)
h11==0.14.0 # via httpcore, uvicorn
h5grove==1.3.0 # via nomad-lab (pyproject.toml)
@@ -72,7 +70,7 @@ isoduration==20.11.0 # via jsonschema
itsdangerous==2.2.0 # via nomad-lab (pyproject.toml)
jinja2==3.1.4 # via jupyterhub, sphinx
jmespath==1.0.1 # via nomad-lab (pyproject.toml)
-joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn
+joblib==1.4.2 # via pymatgen, scikit-learn
jsonpointer==3.0.0 # via jsonschema
jsonschema==4.17.3 # via jupyter-telemetry, oauthenticator, nomad-lab (pyproject.toml)
jupyter-telemetry==0.1.0 # via jupyterhub
@@ -89,28 +87,25 @@ m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic
markupsafe==2.1.5 # via jinja2, mako
matid==2.1.2 # via nomad-lab (pyproject.toml)
-matplotlib==3.9.2 # via ase, mdanalysis, pymatgen
-mda-xdrlib==0.2.0 # via mdanalysis, pyedr
-mdanalysis==2.7.0 # via nomad-lab (pyproject.toml)
+matplotlib==3.9.2 # via ase, pymatgen
+mda-xdrlib==0.2.0 # via pyedr
mistune==3.0.2 # via m2r
-mmtf-python==1.1.3 # via mdanalysis
mongoengine==0.29.0 # via nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade
monty==2024.7.30 # via pymatgen
mpmath==1.3.0 # via sympy
-mrcfile==1.5.3 # via griddataformats
-msgpack==1.0.8 # via mmtf-python, nomad-lab (pyproject.toml)
+msgpack==1.1.0 # via nomad-lab (pyproject.toml)
netcdf4==1.6.5 # via nomad-lab (pyproject.toml)
-networkx==3.3 # via matid, pymatgen, nomad-lab (pyproject.toml)
+networkx==3.3 # via matid, pymatgen
nomad-openbis==1.0.0 # via nomad-lab (pyproject.toml)
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
-numpy==1.26.4 # via ase, cftime, contourpy, griddataformats, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-lab (pyproject.toml)
+numpy==1.26.4 # via ase, cftime, contourpy, h5grove, h5py, matid, matplotlib, netcdf4, nptyping, pandas, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-lab (pyproject.toml)
oauthenticator==15.1.0 # via nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub
openpyxl==3.1.5 # via nomad-lab (pyproject.toml)
optimade==0.22.1 # via nomad-lab (pyproject.toml)
orjson==3.10.7 # via h5grove, nomad-lab (pyproject.toml)
-packaging==24.1 # via deprecation, gunicorn, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, sphinx, xarray
+packaging==24.1 # via deprecation, gunicorn, jupyterhub, matplotlib, mongomock, pint, plotly, sphinx, xarray
palettable==3.3.3 # via pymatgen
pamela==1.2.0 ; sys_platform != 'win32' # via jupyterhub
pandas==2.2.2 # via nomad-openbis, panedr, pymatgen, xarray, nomad-lab (pyproject.toml)
@@ -158,7 +153,7 @@ ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen
ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml
runstats==2.0.0 # via nomad-lab (pyproject.toml)
scikit-learn==1.5.1 # via matid, nomad-lab (pyproject.toml)
-scipy==1.14.1 # via ase, griddataformats, mdanalysis, pymatgen, scikit-learn, nomad-lab (pyproject.toml)
+scipy==1.14.1 # via ase, pymatgen, scikit-learn, nomad-lab (pyproject.toml)
sentinels==1.0.0 # via mongomock
six==1.16.0 # via basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
smmap==5.0.1 # via gitdb
@@ -180,13 +175,13 @@ sympy==1.13.2 # via pymatgen
tabulate==0.8.9 # via nomad-openbis, pymatgen, nomad-lab (pyproject.toml)
tenacity==9.0.0 # via plotly
texttable==1.7.0 # via nomad-openbis
-threadpoolctl==3.5.0 # via mdanalysis, scikit-learn
+threadpoolctl==3.5.0 # via scikit-learn
tifffile==2024.8.30 # via h5grove
toposort==1.10 # via nomad-lab (pyproject.toml)
tornado==6.4.1 # via jupyterhub
-tqdm==4.66.5 # via mdanalysis, pyedr, pymatgen
+tqdm==4.66.5 # via pyedr, pymatgen
traitlets==5.14.3 # via jupyter-telemetry, jupyterhub
-types-python-dateutil==2.9.0.20240821 # via arrow
+types-python-dateutil==2.9.0.20240906 # via arrow
typing-extensions==4.12.2 # via alembic, fastapi, jwcrypto, pydantic, sqlalchemy
typish==1.9.3 # via nptyping
tzdata==2024.1 # via celery, pandas
diff --git a/tests/app/v1/routers/test_systems.py b/tests/app/v1/routers/test_systems.py
index fe261c95348a121c3ec87207d9c0dea6aefc88a5..debb8bdef085c2f6a3950386e9cbb53c7a161309 100644
--- a/tests/app/v1/routers/test_systems.py
+++ b/tests/app/v1/routers/test_systems.py
@@ -225,10 +225,11 @@ REMARK 285 A: 5.000, 0.000, 0.000
REMARK 285 B: 0.000, 5.000, 0.000
REMARK 285 C: 0.000, 0.000, 5.000
REMARK 285 PBC (A, B, C): TRUE, TRUE, TRUE
-CRYST1 5.000 5.000 5.000 90.00 90.00 90.00 P 1 1
-ATOM 1 C UNK X 1 0.000 0.000 0.000 1.00 0.00 C
-ATOM 2 H UNK X 1 1.000 1.000 1.000 1.00 0.00 H
-END
+CRYST1 5.000 5.000 5.000 90.00 90.00 90.00 P 1
+MODEL 1
+ATOM 1 C MOL 1 0.000 0.000 0.000 1.00 0.00 C
+ATOM 2 H MOL 1 1.000 1.000 1.000 1.00 0.00 H
+ENDMDL
""",
'CH.pdb',
id='pdb',
@@ -308,13 +309,10 @@ def test_formats_with_cell(
pytest.param(
'pdb',
"""TITLE NOMAD ENTRY ID: systems_entry_1
-REMARK 285 UNITARY VALUES FOR THE UNIT CELL SET BECAUSE UNIT CELL INFORMATION
-REMARK 285 WAS MISSING. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1
-REMARK 285 RECORD IS INCLUDED, BUT THE VALUES ON THIS RECORD ARE MEANINGLESS.
-CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
-ATOM 1 N UNK X 1 0.000 0.000 0.000 1.00 0.00 N
-ATOM 2 O UNK X 1 1.000 1.000 1.000 1.00 0.00 O
-END
+MODEL 1
+ATOM 1 N MOL 1 0.000 0.000 0.000 1.00 0.00 N
+ATOM 2 O MOL 1 1.000 1.000 1.000 1.00 0.00 O
+ENDMDL
""",
'NO.pdb',
id='pdb',