Loading structure_comparison/vdW_structure.py 0 → 100644 +291 −0 Original line number Diff line number Diff line from typing import Union, List import numpy as np from pymatgen.core.structure import Structure from pymatgen.core.sites import PeriodicSite from pymatgen.core.lattice import Lattice from ase.geometry.geometry import get_layers from layer_shifter import LayerShifter from pymatgen.io.ase import AseAtomsAdaptor from copy import deepcopy class VdWStructure: def __init__(self, structure: Structure, minimum_vdW_gap: Union[int, float]): """Identify van der Waals layers based on if the spacing between atomic layers exceeds the minimum_vdW_gap.""" if not isinstance(structure, Structure): raise TypeError(f"Expected a pymatgen Structure object, got {type(structure).__name__}") if not isinstance(minimum_vdW_gap, (float, int)): raise TypeError(f"Expected a float/int for minimum_vdW_gap, got {type(minimum_vdW_gap).__name__}") self.minimum_vdW_gap = minimum_vdW_gap self.vdW_layers, self.layer_images, self.vdW_spacings = self.get_vdW_layers(structure) #print(self.vdW_layers, self.layer_images, self.vdW_spacings) if len(self.vdW_layers) == 1 and self.vdW_spacings[0] < self.minimum_vdW_gap: raise ValueError(f"No van der Waals layers found with a gap of {minimum_vdW_gap} Å.") self.structure = self.shift_to_vdW_gap(structure, self.vdW_layers, self.layer_images).get_sorted_structure() self.vdW_layers, self.layer_images, self.vdW_spacings = self.get_vdW_layers(self.structure) #print(self.vdW_layers, self.layer_images, self.vdW_spacings) self.ase_atoms_adaptor = AseAtomsAdaptor() self.layer_shifter = LayerShifter() def shift_site(self, site, shift, pos_ind, coords_are_cartesian): shift_vector = [0, 0, 0] shift_vector[pos_ind] = shift if coords_are_cartesian: coordinates = np.add(site.coords, shift_vector) else: coordinates = np.add(site.frac_coords, shift_vector) return coordinates def shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[Union[int, float], List[Union[int, float]]], pos_ind: int, coords_are_cartesian: bool=True): """Shifts vdW_layers provided by layer_inds by a shift amount""" if type(layer_inds) is not list: layer_inds = [layer_inds] if type(shift) is not list: shift = [shift] if len(layer_inds) != len(shift): raise ValueError(f"layer_inds and shift arguments are different lengths!") shifts_dct = {} for ii, i in enumerate(layer_inds): for j in self.vdW_layers[i]: shifts_dct[j] = shift[ii] new_coordinates = [] for site_ind in range(len(self.structure)): if site_ind in list(shifts_dct.keys()): new_coordinates.append(self.shift_site(self.structure[site_ind], shifts_dct[site_ind], pos_ind, coords_are_cartesian)) else: new_coordinates.append(self.shift_site(self.structure[site_ind], 0, pos_ind, coords_are_cartesian)) # no shift shifted_structure = Structure( lattice=self.structure.lattice, coords=new_coordinates, species=[site.specie for site in self.structure], coords_are_cartesian=coords_are_cartesian, to_unit_cell=True ) if not shifted_structure.is_valid(): print(f"Warning: the applied shift(s) has made this structure invalid. Proceed with caution!") return VdWStructure(shifted_structure.get_sorted_structure(), self.minimum_vdW_gap) def x_shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[int, float], coords_are_cartesian: bool=True): return self.shift_vdW_layers(layer_inds, shift, 0, coords_are_cartesian) def y_shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[int, float], coords_are_cartesian: bool=True): return self.shift_vdW_layers(layer_inds, shift, 1, coords_are_cartesian) def z_shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[int, float], coords_are_cartesian: bool=True): return self.shift_vdW_layers(layer_inds, shift, 2, coords_are_cartesian) def z_solve_shift_vdW_layers(self, layer_inds: Union[int, List[int]], solve_shift: Union[int, float], adjust_z_cell: bool=True): ''' Solves for a CARTESIAN shift towards the vdW layer below the structure that yields the solve_shift interlayer distance ''' structure_copy = deepcopy(self.structure) atoms_copy = structure_copy.to_ase_atoms() atom_layer_indices, atom_layer_levels = get_layers(atoms_copy, (0, 0, 1)) if type(layer_inds) is not list: layer_inds = [layer_inds] if type(solve_shift) is not list: solve_shift = [solve_shift] all_shift_vectors = [0, 0, 0] bottom_shift = None for ii, i in enumerate(layer_inds): vdW_atom_layers = [atom_layer_indices[j] for j in self.vdW_layers[i]] min_vdW_atom_layer_number = np.min(vdW_atom_layers) # Get the minimum layer if min_vdW_atom_layer_number == 0: # Handle bottom layer shift differently bottom_shift = solve_shift[ii] else: atoms_copy = self.layer_shifter.structure_shift(atoms_copy, layer_number=min_vdW_atom_layer_number, distance=solve_shift[ii], shift_layers=True, shift_one=False ) current_distance = self.layer_shifter.layer_distance(atom_layer_levels, min_vdW_atom_layer_number) shift_vector = self.layer_shifter.get_shift_vector(atoms_copy, (0, 0, 1), current_distance, solve_shift[ii]) all_shift_vectors = np.subtract(all_shift_vectors, shift_vector) # Increases the z_cell vector magnitude by summed total of the shifts, along the z_cell vector direction shifted_structure = self.ase_atoms_adaptor.get_structure(atoms_copy) if adjust_z_cell == True: shifted_structure_lattice = Lattice(np.array([ shifted_structure.lattice.matrix[0], shifted_structure.lattice.matrix[1], np.add(shifted_structure.lattice.matrix[2], np.array(all_shift_vectors)) ])) shifted_structure = Structure(lattice=shifted_structure_lattice, coords=[site.coords for site in shifted_structure], species=[site.specie for site in shifted_structure], coords_are_cartesian=True, to_unit_cell=False ) if bottom_shift: shifted_atoms = shifted_structure.to_ase_atoms() shifted_atoms.center(vacuum=0.5 * bottom_shift, axis=2) shifted_structure = self.ase_atoms_adaptor.get_structure(shifted_atoms) if not shifted_structure.is_valid(): print(f"Warning: the applied shift(s) has made this structure invalid. Proceed with caution!") return VdWStructure(shifted_structure.get_sorted_structure(), self.minimum_vdW_gap) def set_vacuum(self, vacuum: Union[int, float]): structure_copy = deepcopy(self.structure) atoms_copy = self.structure.to_ase_atoms() atoms_copy.center(vacuum=0.5 * vacuum, axis=2) vacuum_structure = self.ase_atoms_adaptor.get_structure(atoms_copy) return VdWStructure(vacuum_structure.get_sorted_structure(), self.minimum_vdW_gap) def get_vdW_layers(self, structure: Structure): """Identify van der Waals layers in the structure based on spacing along the z-direction.""" vdW_layers = [[]] z_images = [[]] vdW_spacings = [] z_magnitude = structure.lattice.c all_zs, all_indices = [s.coords[2] for s in structure], [i for i, site in enumerate(structure)] zipped = zip(all_zs, all_indices) s_zipped = sorted(zipped, key=lambda x: x[0]) zs, idxs = zip(*s_zipped) diffs = [z_magnitude - zs[-1] + zs[0]] + [zs[i+1] - zs[i] for i in range(len(zs)-1)] count = 0 for i, diff in enumerate(diffs): if diff > self.minimum_vdW_gap: vdW_spacings.append(diff) vdW_layers.append([]) z_images.append([]) count += 1 vdW_layers[count].append(idxs[i]) z_images[count].append(0) # Handle periodic boundary conditions if count > 0 and diffs[0] < self.minimum_vdW_gap: z_images[0] = [-1] * len(vdW_layers[0]) + [0] * len(vdW_layers[-1]) # Change image number here vdW_layers[0] += vdW_layers[-1] vdW_layers.pop() z_images.pop() # Clean up empty layers cleaned_layers = [layer for layer in vdW_layers if layer] cleaned_images = [z_images[i] for i, layer in enumerate(vdW_layers) if layer] return cleaned_layers, cleaned_images, vdW_spacings def shift_to_vdW_gap(self, structure: Structure, layers: List[int], images: List[int]): """Shift the structure to ensure periodic boundaries fall in vdW gaps.""" for layer_index, layer in enumerate(layers): for i, site_ind in enumerate(layer): if images[layer_index][i] != 0: shift_factor = np.negative(images[layer_index][i]) shift = np.multiply(shift_factor, structure.lattice.matrix[2]) structure[site_ind].coords += shift zs = [site.coords[2] for site in structure] padding = (structure.lattice.c - (max(zs) - min(zs))) / 2 z_shift = structure.lattice.c - padding - max(zs) for site in structure: site.coords += z_shift return Structure( lattice=structure.lattice, coords=[site.coords for site in structure], species=[site.specie for site in structure], coords_are_cartesian=True, to_unit_cell=True ).get_sorted_structure() def _add_vdW_sites(self, new_layer_numbers: List[int]): """Adds z-direction spacing to the new lattice and adds sites with appropriate spacing.""" new_sites = [] new_lattice = Lattice(np.array([ self.structure.lattice.matrix[0], self.structure.lattice.matrix[1], np.multiply(len(new_layer_numbers) + 1, self.structure.lattice.matrix[2]) ])) for new_layer_number_ind, new_layer_number in enumerate(new_layer_numbers): for site_number in self.vdW_layers[new_layer_number]: site_shift = np.multiply(new_layer_number_ind, self.structure.lattice.matrix[2]) coords = self.structure[site_number].coords + site_shift species = self.structure[site_number].species site = PeriodicSite( species=species, coords=coords, lattice=new_lattice, coords_are_cartesian=True ) new_sites.append(site) new_structure = Structure( lattice=new_lattice, coords=[site.coords for site in new_sites], species=[site.specie for site in new_sites], coords_are_cartesian=True, to_unit_cell=True ) return new_structure.get_sorted_structure() def _rescale_vdW_lattice(self, new_layer_numbers: List[int], new_structure: Structure): """Correct the vdW spacing in the new structure with the extended lattice.""" new_structure_atoms = new_structure.to_ase_atoms() new_layers, new_shifts, new_spacings = self.get_vdW_layers(new_structure) new_indices, new_levels = get_layers(new_structure_atoms, (0, 0, 1)) # Perform the correct layer shifts for each layer for upper_layer_ind, upper_layer_number in enumerate(new_layers[1:]): # Skip bottom layer shift_layer_number = new_indices[upper_layer_number[0]] layer_to_get_shift = new_layer_numbers[upper_layer_ind + 1] shift = self.vdW_spacings[layer_to_get_shift] new_structure_atoms = self.layer_shifter.structure_shift( new_structure_atoms, layer_number=shift_layer_number, distance=shift, shift_layers=True, shift_one=False ) # Create the appropriate Lattice and Structure new_structure = self.ase_atoms_adaptor.get_structure(new_structure_atoms) newest_indices, newest_levels = get_layers(new_structure_atoms, (0, 0, 1)) z_magnitude = newest_levels[-1] - newest_levels[0] + self.vdW_spacings[new_layer_numbers[0]] newest_z = z_magnitude * (self.structure.lattice.matrix[2] / np.linalg.norm(self.structure.lattice.matrix[2])) newest_lattice = Lattice(np.array([ self.structure.lattice.matrix[0], self.structure.lattice.matrix[1], newest_z ])) coord_shift = [0, 0, 0.5 * self.vdW_spacings[new_layer_numbers[0]] - new_structure[0].coords[2]] newest_structure = Structure( lattice=newest_lattice, coords=[site.coords + coord_shift for site in new_structure], species=[site.specie for site in new_structure], coords_are_cartesian=True, to_unit_cell=True ) return newest_structure.get_sorted_structure() def extend_vdW_layers(self, new_layer_numbers: List[int]): """Extend the vdW layers by duplicating specified layers into a new structure. Returns VdWBulk.""" for new_layer_number in new_layer_numbers: if new_layer_number not in range(len(self.vdW_layers)): raise IndexError(f"vdW layer index {new_layer_number} is not valid for vdW_layers of len({len(self.vdW_layers)})!") no_spacing_extended_structure = self._add_vdW_sites(new_layer_numbers) correct_spacing_structure = self._rescale_vdW_lattice(new_layer_numbers, no_spacing_extended_structure) return VdWStructure(correct_spacing_structure.get_sorted_structure(), self.minimum_vdW_gap) No newline at end of file Loading
structure_comparison/vdW_structure.py 0 → 100644 +291 −0 Original line number Diff line number Diff line from typing import Union, List import numpy as np from pymatgen.core.structure import Structure from pymatgen.core.sites import PeriodicSite from pymatgen.core.lattice import Lattice from ase.geometry.geometry import get_layers from layer_shifter import LayerShifter from pymatgen.io.ase import AseAtomsAdaptor from copy import deepcopy class VdWStructure: def __init__(self, structure: Structure, minimum_vdW_gap: Union[int, float]): """Identify van der Waals layers based on if the spacing between atomic layers exceeds the minimum_vdW_gap.""" if not isinstance(structure, Structure): raise TypeError(f"Expected a pymatgen Structure object, got {type(structure).__name__}") if not isinstance(minimum_vdW_gap, (float, int)): raise TypeError(f"Expected a float/int for minimum_vdW_gap, got {type(minimum_vdW_gap).__name__}") self.minimum_vdW_gap = minimum_vdW_gap self.vdW_layers, self.layer_images, self.vdW_spacings = self.get_vdW_layers(structure) #print(self.vdW_layers, self.layer_images, self.vdW_spacings) if len(self.vdW_layers) == 1 and self.vdW_spacings[0] < self.minimum_vdW_gap: raise ValueError(f"No van der Waals layers found with a gap of {minimum_vdW_gap} Å.") self.structure = self.shift_to_vdW_gap(structure, self.vdW_layers, self.layer_images).get_sorted_structure() self.vdW_layers, self.layer_images, self.vdW_spacings = self.get_vdW_layers(self.structure) #print(self.vdW_layers, self.layer_images, self.vdW_spacings) self.ase_atoms_adaptor = AseAtomsAdaptor() self.layer_shifter = LayerShifter() def shift_site(self, site, shift, pos_ind, coords_are_cartesian): shift_vector = [0, 0, 0] shift_vector[pos_ind] = shift if coords_are_cartesian: coordinates = np.add(site.coords, shift_vector) else: coordinates = np.add(site.frac_coords, shift_vector) return coordinates def shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[Union[int, float], List[Union[int, float]]], pos_ind: int, coords_are_cartesian: bool=True): """Shifts vdW_layers provided by layer_inds by a shift amount""" if type(layer_inds) is not list: layer_inds = [layer_inds] if type(shift) is not list: shift = [shift] if len(layer_inds) != len(shift): raise ValueError(f"layer_inds and shift arguments are different lengths!") shifts_dct = {} for ii, i in enumerate(layer_inds): for j in self.vdW_layers[i]: shifts_dct[j] = shift[ii] new_coordinates = [] for site_ind in range(len(self.structure)): if site_ind in list(shifts_dct.keys()): new_coordinates.append(self.shift_site(self.structure[site_ind], shifts_dct[site_ind], pos_ind, coords_are_cartesian)) else: new_coordinates.append(self.shift_site(self.structure[site_ind], 0, pos_ind, coords_are_cartesian)) # no shift shifted_structure = Structure( lattice=self.structure.lattice, coords=new_coordinates, species=[site.specie for site in self.structure], coords_are_cartesian=coords_are_cartesian, to_unit_cell=True ) if not shifted_structure.is_valid(): print(f"Warning: the applied shift(s) has made this structure invalid. Proceed with caution!") return VdWStructure(shifted_structure.get_sorted_structure(), self.minimum_vdW_gap) def x_shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[int, float], coords_are_cartesian: bool=True): return self.shift_vdW_layers(layer_inds, shift, 0, coords_are_cartesian) def y_shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[int, float], coords_are_cartesian: bool=True): return self.shift_vdW_layers(layer_inds, shift, 1, coords_are_cartesian) def z_shift_vdW_layers(self, layer_inds: Union[int, List[int]], shift: Union[int, float], coords_are_cartesian: bool=True): return self.shift_vdW_layers(layer_inds, shift, 2, coords_are_cartesian) def z_solve_shift_vdW_layers(self, layer_inds: Union[int, List[int]], solve_shift: Union[int, float], adjust_z_cell: bool=True): ''' Solves for a CARTESIAN shift towards the vdW layer below the structure that yields the solve_shift interlayer distance ''' structure_copy = deepcopy(self.structure) atoms_copy = structure_copy.to_ase_atoms() atom_layer_indices, atom_layer_levels = get_layers(atoms_copy, (0, 0, 1)) if type(layer_inds) is not list: layer_inds = [layer_inds] if type(solve_shift) is not list: solve_shift = [solve_shift] all_shift_vectors = [0, 0, 0] bottom_shift = None for ii, i in enumerate(layer_inds): vdW_atom_layers = [atom_layer_indices[j] for j in self.vdW_layers[i]] min_vdW_atom_layer_number = np.min(vdW_atom_layers) # Get the minimum layer if min_vdW_atom_layer_number == 0: # Handle bottom layer shift differently bottom_shift = solve_shift[ii] else: atoms_copy = self.layer_shifter.structure_shift(atoms_copy, layer_number=min_vdW_atom_layer_number, distance=solve_shift[ii], shift_layers=True, shift_one=False ) current_distance = self.layer_shifter.layer_distance(atom_layer_levels, min_vdW_atom_layer_number) shift_vector = self.layer_shifter.get_shift_vector(atoms_copy, (0, 0, 1), current_distance, solve_shift[ii]) all_shift_vectors = np.subtract(all_shift_vectors, shift_vector) # Increases the z_cell vector magnitude by summed total of the shifts, along the z_cell vector direction shifted_structure = self.ase_atoms_adaptor.get_structure(atoms_copy) if adjust_z_cell == True: shifted_structure_lattice = Lattice(np.array([ shifted_structure.lattice.matrix[0], shifted_structure.lattice.matrix[1], np.add(shifted_structure.lattice.matrix[2], np.array(all_shift_vectors)) ])) shifted_structure = Structure(lattice=shifted_structure_lattice, coords=[site.coords for site in shifted_structure], species=[site.specie for site in shifted_structure], coords_are_cartesian=True, to_unit_cell=False ) if bottom_shift: shifted_atoms = shifted_structure.to_ase_atoms() shifted_atoms.center(vacuum=0.5 * bottom_shift, axis=2) shifted_structure = self.ase_atoms_adaptor.get_structure(shifted_atoms) if not shifted_structure.is_valid(): print(f"Warning: the applied shift(s) has made this structure invalid. Proceed with caution!") return VdWStructure(shifted_structure.get_sorted_structure(), self.minimum_vdW_gap) def set_vacuum(self, vacuum: Union[int, float]): structure_copy = deepcopy(self.structure) atoms_copy = self.structure.to_ase_atoms() atoms_copy.center(vacuum=0.5 * vacuum, axis=2) vacuum_structure = self.ase_atoms_adaptor.get_structure(atoms_copy) return VdWStructure(vacuum_structure.get_sorted_structure(), self.minimum_vdW_gap) def get_vdW_layers(self, structure: Structure): """Identify van der Waals layers in the structure based on spacing along the z-direction.""" vdW_layers = [[]] z_images = [[]] vdW_spacings = [] z_magnitude = structure.lattice.c all_zs, all_indices = [s.coords[2] for s in structure], [i for i, site in enumerate(structure)] zipped = zip(all_zs, all_indices) s_zipped = sorted(zipped, key=lambda x: x[0]) zs, idxs = zip(*s_zipped) diffs = [z_magnitude - zs[-1] + zs[0]] + [zs[i+1] - zs[i] for i in range(len(zs)-1)] count = 0 for i, diff in enumerate(diffs): if diff > self.minimum_vdW_gap: vdW_spacings.append(diff) vdW_layers.append([]) z_images.append([]) count += 1 vdW_layers[count].append(idxs[i]) z_images[count].append(0) # Handle periodic boundary conditions if count > 0 and diffs[0] < self.minimum_vdW_gap: z_images[0] = [-1] * len(vdW_layers[0]) + [0] * len(vdW_layers[-1]) # Change image number here vdW_layers[0] += vdW_layers[-1] vdW_layers.pop() z_images.pop() # Clean up empty layers cleaned_layers = [layer for layer in vdW_layers if layer] cleaned_images = [z_images[i] for i, layer in enumerate(vdW_layers) if layer] return cleaned_layers, cleaned_images, vdW_spacings def shift_to_vdW_gap(self, structure: Structure, layers: List[int], images: List[int]): """Shift the structure to ensure periodic boundaries fall in vdW gaps.""" for layer_index, layer in enumerate(layers): for i, site_ind in enumerate(layer): if images[layer_index][i] != 0: shift_factor = np.negative(images[layer_index][i]) shift = np.multiply(shift_factor, structure.lattice.matrix[2]) structure[site_ind].coords += shift zs = [site.coords[2] for site in structure] padding = (structure.lattice.c - (max(zs) - min(zs))) / 2 z_shift = structure.lattice.c - padding - max(zs) for site in structure: site.coords += z_shift return Structure( lattice=structure.lattice, coords=[site.coords for site in structure], species=[site.specie for site in structure], coords_are_cartesian=True, to_unit_cell=True ).get_sorted_structure() def _add_vdW_sites(self, new_layer_numbers: List[int]): """Adds z-direction spacing to the new lattice and adds sites with appropriate spacing.""" new_sites = [] new_lattice = Lattice(np.array([ self.structure.lattice.matrix[0], self.structure.lattice.matrix[1], np.multiply(len(new_layer_numbers) + 1, self.structure.lattice.matrix[2]) ])) for new_layer_number_ind, new_layer_number in enumerate(new_layer_numbers): for site_number in self.vdW_layers[new_layer_number]: site_shift = np.multiply(new_layer_number_ind, self.structure.lattice.matrix[2]) coords = self.structure[site_number].coords + site_shift species = self.structure[site_number].species site = PeriodicSite( species=species, coords=coords, lattice=new_lattice, coords_are_cartesian=True ) new_sites.append(site) new_structure = Structure( lattice=new_lattice, coords=[site.coords for site in new_sites], species=[site.specie for site in new_sites], coords_are_cartesian=True, to_unit_cell=True ) return new_structure.get_sorted_structure() def _rescale_vdW_lattice(self, new_layer_numbers: List[int], new_structure: Structure): """Correct the vdW spacing in the new structure with the extended lattice.""" new_structure_atoms = new_structure.to_ase_atoms() new_layers, new_shifts, new_spacings = self.get_vdW_layers(new_structure) new_indices, new_levels = get_layers(new_structure_atoms, (0, 0, 1)) # Perform the correct layer shifts for each layer for upper_layer_ind, upper_layer_number in enumerate(new_layers[1:]): # Skip bottom layer shift_layer_number = new_indices[upper_layer_number[0]] layer_to_get_shift = new_layer_numbers[upper_layer_ind + 1] shift = self.vdW_spacings[layer_to_get_shift] new_structure_atoms = self.layer_shifter.structure_shift( new_structure_atoms, layer_number=shift_layer_number, distance=shift, shift_layers=True, shift_one=False ) # Create the appropriate Lattice and Structure new_structure = self.ase_atoms_adaptor.get_structure(new_structure_atoms) newest_indices, newest_levels = get_layers(new_structure_atoms, (0, 0, 1)) z_magnitude = newest_levels[-1] - newest_levels[0] + self.vdW_spacings[new_layer_numbers[0]] newest_z = z_magnitude * (self.structure.lattice.matrix[2] / np.linalg.norm(self.structure.lattice.matrix[2])) newest_lattice = Lattice(np.array([ self.structure.lattice.matrix[0], self.structure.lattice.matrix[1], newest_z ])) coord_shift = [0, 0, 0.5 * self.vdW_spacings[new_layer_numbers[0]] - new_structure[0].coords[2]] newest_structure = Structure( lattice=newest_lattice, coords=[site.coords + coord_shift for site in new_structure], species=[site.specie for site in new_structure], coords_are_cartesian=True, to_unit_cell=True ) return newest_structure.get_sorted_structure() def extend_vdW_layers(self, new_layer_numbers: List[int]): """Extend the vdW layers by duplicating specified layers into a new structure. Returns VdWBulk.""" for new_layer_number in new_layer_numbers: if new_layer_number not in range(len(self.vdW_layers)): raise IndexError(f"vdW layer index {new_layer_number} is not valid for vdW_layers of len({len(self.vdW_layers)})!") no_spacing_extended_structure = self._add_vdW_sites(new_layer_numbers) correct_spacing_structure = self._rescale_vdW_lattice(new_layer_numbers, no_spacing_extended_structure) return VdWStructure(correct_spacing_structure.get_sorted_structure(), self.minimum_vdW_gap) No newline at end of file
