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--- Ogre_original_version/Ogre/ogre/utils/utils.py 2025-11-02 15:00:14.132902503 +0100
+++ Ogre_version_OK/ogre/utils/utils.py 2025-10-26 13:52:14.000000000 +0100
@@ -30,8 +30,11 @@
"""
file_name = working_dir + "/temp.POSCAR.vasp"
io.write(file_name, images,parallel=False)
- modify_poscar(file_name)
- slab = mg.Structure.from_file(file_name)
+ io.write(file_name+'_before_modify_poscar', images, parallel=False)
+ #modify_poscar(file_name)
+
+ print('calling mg.core.Structure.from_file with arg:', file_name, type(file_name))
+ slab = mg.core.Structure.from_file(file_name)
os.remove(file_name)
return slab
@@ -267,7 +270,7 @@
continue
species = [slab_supercell_sg.structure[n].specie
for n in subgraph.nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules.append(molecule)
# molecules are the list of molecules that need to be moved
move_list = []
@@ -349,7 +352,7 @@
sites = []
for slab_molecule in slab_molecules:
for curr_site in slab_molecule:
- curr_site = mg.PeriodicSite(curr_site.specie,
+ curr_site = PeriodicSite(curr_site.specie,
curr_site.coords,
slab.lattice,
coords_are_cartesian=True)
@@ -650,7 +653,7 @@
with open(output_file, 'w') as final_file_1:
for i in range(len(lines)):
final_file_1.writelines(lines[i])
- structure = mg.Structure.from_file(output_file)
+ structure = mg.core.Structure.from_file(output_file)
lattice = Lattice(structure.lattice.matrix)
frac_coords = lattice.get_fractional_coords(structure.cart_coords)
for i in range(frac_coords.shape[0]):
@@ -703,8 +706,10 @@
Molecules that are correlated to the subgraphs.
"""
bulk_super_structure_sg_graph = nx.Graph(bulk_structure_sg.graph)
- all_super_subgraphs = list(nx.connected_component_subgraphs
- (bulk_super_structure_sg_graph))
+ G = bulk_super_structure_sg_graph
+ # all_super_subgraphs = list(nx.connected_component_subgraphs
+ # (bulk_super_structure_sg_graph))
+ all_super_subgraphs = [G.subgraph(c).copy() for c in nx.connected_components(G)]
super_subgraphs = []
for subgraph in all_super_subgraphs:
in_boundary = any([d['to_jimage'] == (0, 0, 0)
@@ -725,7 +730,7 @@
for n in subgraph.nodes()]
species = [bulk_structure_sg.structure[n].specie
for n in subgraph.nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules.append(molecule)
return super_subgraphs, molecules
@@ -761,7 +766,7 @@
for n in subgraph.nodes()]
species = [bulk_structure_sg.structure[n].specie
for n in subgraph.nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules.append(molecule)
return all_super_subgraphs, molecules
@@ -789,8 +794,10 @@
Molecules that are correlated to the subgraphs.
"""
bulk_super_structure_sg_graph = nx.Graph(bulk_structure_sg.graph)
- all_super_subgraphs = list(nx.connected_component_subgraphs
- (bulk_super_structure_sg_graph))
+ # all_super_subgraphs = list(nx.connected_component_subgraphs
+ # (bulk_super_structure_sg_graph))
+ G = bulk_super_structure_sg_graph
+ all_super_subgraphs = [G.subgraph(c).copy() for c in nx.connected_components(G)]
for subgraph in all_super_subgraphs:
for n in subgraph:
subgraph.add_node(n,
@@ -836,7 +843,7 @@
for n in subgraph.nodes()]
species = [bulk_structure_sg.structure[n].specie
for n in subgraph.nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules.append(molecule)
return delta, all_super_subgraphs, molecules
@@ -890,7 +897,7 @@
for n in subgraph.nodes()]
species = [bulk_structure_sg.structure[n].specie
for n in subgraph.nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules.append(molecule)
return unique_super_subgraphs, molecules
@@ -913,7 +920,7 @@
are different from those in bulk. In this function,
we would only find the different subgraphs based on its species.
slab_molecules : list
- [slab_molecule, ...], slab_molecule is the mg.Molecule of diffenert_subgraphs.
+ [slab_molecule, ...], slab_molecule is the mg.core.Molecule of diffenert_subgraphs.
"""
slab_supercell_sg_graph = nx.Graph(slab_supercell_sg.graph)
all_subgraphs = list(nx.connected_component_subgraphs
@@ -946,7 +953,7 @@
for n in subgraph.nodes()]
species = [slab_supercell_sg.structure[n].specie
for n in subgraph.nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
slab_molecules.append(molecule)
return different_subgraphs, slab_molecules
@@ -1238,7 +1245,7 @@
for new_relative in new_relatives]
species = [bulk_super_structure_sg.structure[n].specie
for n in qualified_unique_subgraphs[i].nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules_new.append(molecule)
sites = []
molecules_new_backup = list(molecules_new)
@@ -1247,7 +1254,7 @@
while i < len(molecules_new):
under = False
for curr_site in molecules_new[i]:
- curr_site = mg.PeriodicSite(curr_site.specie,
+ curr_site = PeriodicSite(curr_site.specie,
curr_site.coords,
slab.lattice,
coords_are_cartesian=True)
@@ -1261,7 +1268,7 @@
molecules_new = molecules_new_backup
for molecule in molecules_new:
for curr_site in molecule:
- curr_site = mg.PeriodicSite(curr_site.specie,
+ curr_site = PeriodicSite(curr_site.specie,
curr_site.coords,
slab.lattice,
coords_are_cartesian=True)
@@ -1284,10 +1291,10 @@
for j in range(coords.shape[1]):
coords[i, j] = coords[i, j] % 1
species = slab.species
- molecule = mg.Molecule(species, coords)
+ molecule = mg.core.Molecule(species, coords)
sites = []
for site in molecule:
- site = mg.PeriodicSite(site.specie,
+ site = PeriodicSite(site.specie,
site.coords,
slab.lattice)
tmp = [site.is_periodic_image(item, tolerance=1e-5) for item in sites]
@@ -1439,7 +1446,7 @@
for new_relative in new_relatives]
species = [bulk_super_structure_sg.structure[n].specie
for n in less_intact_subgraphs[i].nodes()]
- molecule = mg.Molecule(species=species, coords=coords)
+ molecule = mg.core.Molecule(species=species, coords=coords)
molecules_new.append(molecule)
sites = []
molecules_new_backup = list(molecules_new)
@@ -1448,7 +1455,7 @@
while i < len(molecules_new):
under = False
for curr_site in molecules_new[i]:
- curr_site = mg.PeriodicSite(curr_site.specie,
+ curr_site = PeriodicSite(curr_site.specie,
curr_site.coords,
slab.lattice,
coords_are_cartesian=True)
@@ -1462,7 +1469,7 @@
molecules_new = molecules_new_backup
for molecule in molecules_new:
for curr_site in molecule:
- curr_site = mg.PeriodicSite(curr_site.specie,
+ curr_site = PeriodicSite(curr_site.specie,
curr_site.coords,
slab.lattice,
coords_are_cartesian=True)
@@ -1617,7 +1624,7 @@
slab_delete_layer.center(vacuum=vacuum_size, axis=2)
io.write(file_name, images=slab_delete_layer,parallel=False)
modify_poscar(file_name)
- slab_delete = mg.Structure.from_file(file_name)
+ slab_delete = mg.core.Structure.from_file(file_name)
os.remove(file_name)
return slab_delete
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