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Commit c4035ca2 authored by Dinga Wonanke's avatar Dinga Wonanke Committed by Lauri Himanen
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Improved the handling of layered systems in PorosityNormalizer.

parent 9331f171
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1 merge request!1475Resolve "Processing MOF data problems"
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nomad/normalizing/mof_deconstructor.py
+ 200
− 58
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......@@ -231,6 +231,13 @@ def dfsutil_graph_method(graph, temp, node, visited):
return temp
def longest_list(lst):
'''
return longest list in list of list
'''
return max(lst, key=len)
def remove_unbound_guest(ase_atom):
'''
A simple script to remove guest from a metal organic framework.
......@@ -264,7 +271,6 @@ def remove_unbound_guest(ase_atom):
pymat_graph = connected_components(coordination_graph)
if len(pymat_graph) == 1:
polymeric_indices.append(i)
if len(polymeric_indices) > 0:
Graphs = [StructureGraph.with_local_env_strategy(AseAtomsAdaptor.get_structure(
ase_atom[fragments[i]]), JmolNN()) for i in polymeric_indices]
......@@ -278,9 +284,12 @@ def remove_unbound_guest(ase_atom):
mof_indices = []
for frag_indices in temp_indices:
mof_indices.extend(fragments[frag_indices])
return mof_indices
if len(mof_indices) == 0:
return longest_list(fragments)
else:
return mof_indices
else:
return sum(sum(fragments, []))
return sum(fragments, [])
def connected_components(graph):
......@@ -528,6 +537,68 @@ def find_carbonyl_sulphate(ase_atom):
return sulphate
def find_sulfides(ase_atom):
'''
A simple aglorimth to search for sulfides.
S
|
-C
|
S
Parameters:
-----------
ase_atom: ASE atom
Returns
-------
dictionary of key = carbon index and values = sulphur index
'''
graph, _ = compute_ase_neighbour(ase_atom)
sulfides = {}
for atoms in ase_atom:
if atoms.symbol == 'C':
index = atoms.index
sulphure_atoms = [i for i in graph[index]
if ase_atom[i].symbol == 'S']
if len(sulphure_atoms) == 2:
sulphure_to_metal = sum(
[[j for j in graph[i] if ase_atom[j].symbol in transition_metals()] for i in sulphure_atoms], [])
if len(sulphure_to_metal) > 0:
sulfides[index] = sulphure_atoms
return sulfides
def find_phosphate(ase_atom):
'''
A simple algorithm to search for Carbonyl sulphate found in the system.
O
|
-P-o
|
O
Parameters:
-----------
ase_atom: ASE atom
Returns
-------
dictionary of key = carbon index and values = oxygen index
'''
graph, _ = compute_ase_neighbour(ase_atom)
phosphate = {}
for atoms in ase_atom:
if atoms.symbol == 'P':
index = atoms.index
oxygen = [i for i in graph[index] if ase_atom[i].symbol == 'O']
if len(oxygen) >= 1:
oxy_metal = sum(
[[j for j in graph[i] if ase_atom[j].symbol in transition_metals()] for i in oxygen], [])
if len(oxy_metal) > 0:
phosphate[index] = oxygen
return phosphate
def secondary_building_units(ase_atom):
"""
1) Search for all carboxylate that are connected to a metal.
......@@ -553,8 +624,13 @@ def secondary_building_units(ase_atom):
bonds_to_break = []
carboxylates = find_carboxylates(ase_atom)
all_sulphates = find_carbonyl_sulphate(ase_atom)
all_sulfides = find_sulfides(ase_atom)
all_phosphates = find_phosphate(ase_atom)
seen_phosphorous = []
seen_carbon = []
for atoms in graph:
if atoms in list(carboxylates.keys()):
seen_carbon.append(atoms)
connected = graph[atoms]
all_carbon_indices = [
i for i in connected if ase_atom[i].symbol == 'C']
......@@ -570,15 +646,34 @@ def secondary_building_units(ase_atom):
bonds_to_break.append([atoms] + S_indx)
atom_pairs_at_breaking_point[atoms] = S_indx[0]
if ase_atom[atoms].symbol == 'C':
if atoms in list(all_sulfides.keys()):
seen_carbon.append(atoms)
connected = graph[atoms]
oxygens = [i for i in connected if ase_atom[i].symbol == 'O']
if len(oxygens) == 1:
oxy_metal = [
i for i in oxygens if ase_atom[i].symbol in transition_metals()]
if len(oxy_metal) == 1:
atom_pairs_at_breaking_point[oxygens[0]] = oxy_metal[0]
bonds_to_break.append([oxygens] + oxy_metal)
all_carbon_indices = [
i for i in connected if ase_atom[i].symbol == 'C']
all_nitrogens = [i for i in connected if ase_atom[i].symbol == 'N']
# S_indx = [i for i in connected if ase_atom[i].symbol == 'S']
if len(all_carbon_indices) == 1:
bonds_to_break.append([atoms] + all_carbon_indices)
atom_pairs_at_breaking_point[atoms] = all_carbon_indices[0]
if len(all_nitrogens) == 1:
bonds_to_break.append([atoms] + all_nitrogens)
atom_pairs_at_breaking_point[atoms] = all_nitrogens[0]
# if len(S_indx) == 1:
# bonds_to_break.append([atoms] + S_indx)
# atom_pairs_at_breaking_point[atoms] = S_indx[0]
if ase_atom[atoms].symbol == 'C':
if atoms not in seen_carbon:
connected = graph[atoms]
oxygens = [i for i in connected if ase_atom[i].symbol == 'O']
if len(oxygens) == 1:
oxy_metal = [
i for i in oxygens if ase_atom[i].symbol in transition_metals()]
oxy_metal = [
i for i in oxy_metal if i not in porphyrin_checker]
if len(oxy_metal) == 1:
atom_pairs_at_breaking_point[oxygens[0]] = oxy_metal[0]
bonds_to_break.append([oxygens] + oxy_metal)
if atoms in list(all_sulphates.keys()):
connected = graph[atoms]
......@@ -592,6 +687,7 @@ def secondary_building_units(ase_atom):
for oxy in oxygen:
metal = [i for i in graph[oxy]
if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
if len(metal) > 0:
for met in metal:
atom_pairs_at_breaking_point[oxy] = met
......@@ -599,11 +695,13 @@ def secondary_building_units(ase_atom):
if ase_atom[atoms].symbol == 'O':
seen = sum(list(carboxylates.values())
+ list(all_sulphates.values()), [])
+ list(all_sulphates.values())
+ list(all_phosphates.values()), [])
if atoms not in seen:
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
Nitrogen = [i for i in connected if ase_atom[i].symbol == 'N']
carbon = [i for i in connected if ase_atom[i].symbol
== 'C' and i not in list(carboxylates.keys())]
......@@ -638,13 +736,32 @@ def secondary_building_units(ase_atom):
bonds_to_break.append([atoms] + metal)
if ase_atom[atoms].symbol == 'S':
seen = sum(list(all_sulfides.values()), [])
if atoms not in seen:
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
if len(metal) > 0:
for met in metal:
atom_pairs_at_breaking_point[atoms] = met
bonds_to_break.append([atoms, met])
if atoms in list(all_phosphates.keys()):
seen_phosphorous.append(atoms)
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
if len(metal) > 0:
for met in metal:
atom_pairs_at_breaking_point[atoms] = met
bonds_to_break.append([atoms, met])
all_carbon_indices = [
i for i in connected if ase_atom[i].symbol == 'C']
all_nitrogens = [i for i in connected if ase_atom[i].symbol == 'N']
S_indx = [i for i in connected if ase_atom[i].symbol == 'S']
if len(all_carbon_indices) == 1:
bonds_to_break.append([atoms] + all_carbon_indices)
atom_pairs_at_breaking_point[atoms] = all_carbon_indices[0]
if len(all_nitrogens) == 1:
bonds_to_break.append([atoms] + all_nitrogens)
atom_pairs_at_breaking_point[atoms] = all_nitrogens[0]
if len(S_indx) == 1:
bonds_to_break.append([atoms] + S_indx)
atom_pairs_at_breaking_point[atoms] = S_indx[0]
if ase_atom[atoms].symbol == 'P':
'''
......@@ -653,23 +770,26 @@ def secondary_building_units(ase_atom):
2) Look for all it's neigbours
3) Look for neigbours that are not connected to metal or hydrogen.
'''
connected = graph[atoms]
# not_connected_to_metal_or_hygrogen = [[i for i in graph[j] if ase_atom[i].symbol not in transition_metals() or ase_atom[i].symbol != 'H'] for j in connected]
# seen = list(all_phosphates.keys())
if atoms not in seen_phosphorous:
connected = graph[atoms]
# not_connected_to_metal_or_hygrogen = [[i for i in graph[j] if ase_atom[i].symbol not in transition_metals() or ase_atom[i].symbol != 'H'] for j in connected]
metal_oxy = [[i for i in graph[j] if ase_atom[i].symbol in transition_metals()]
for j in connected]
metal_oxy = [[i for i in graph[j] if ase_atom[i].symbol in transition_metals()]
for j in connected]
metal = sum(metal_oxy, [])
closest_atoms = sum(
[[i for i in graph[j] if i != atoms and not ase_atom[i].symbol in transition_metals()] for j in connected], [])
metal = sum(metal_oxy, [])
metal = [i for i in metal if i not in porphyrin_checker]
closest_atoms = sum(
[[i for i in graph[j] if i != atoms and not ase_atom[i].symbol in transition_metals()] for j in connected], [])
if len(metal) > 0:
all_carbon_indices = sum([[i for i in graph[j] if i in connected]
for j in closest_atoms], [])
for frag in all_carbon_indices:
atom_pairs_at_breaking_point[atoms] = frag
atom_pairs_at_breaking_point[frag] = atoms
bonds_to_break.append([atoms, frag])
if len(metal) > 0:
all_carbon_indices = sum([[i for i in graph[j] if i in connected]
for j in closest_atoms], [])
for frag in all_carbon_indices:
atom_pairs_at_breaking_point[atoms] = frag
atom_pairs_at_breaking_point[frag] = atoms
bonds_to_break.append([atoms, frag])
if ase_atom[atoms].symbol == 'B':
'''
......@@ -681,6 +801,7 @@ def secondary_building_units(ase_atom):
for j in connected]
metal_connect = sum(metal_oxy, [])
metal = [i for i in metal if i not in porphyrin_checker]
if len(metal_connect) > 0:
for frag in metal_connect:
atom_pairs_at_breaking_point[frag[0]] = frag[1]
......@@ -737,15 +858,18 @@ def ligands_and_metal_clusters(ase_atom):
bonds_to_break = []
carboxylates = find_carboxylates(ase_atom)
all_sulphates = find_carbonyl_sulphate(ase_atom)
Seen_oxygen = []
all_sulfides = find_sulfides(ase_atom)
all_phosphates = find_phosphate(ase_atom)
seen_sulphure = sum(list(all_sulfides.values()), [])
for atoms in graph:
if atoms in list(carboxylates.keys()):
oxygen = carboxylates[atoms]
for oxy in oxygen:
metal = [i for i in graph[oxy]
if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
if len(metal) > 0:
Seen_oxygen.append(oxy)
for met in metal:
bonds_to_break.append([atoms] + [met])
atom_pairs_at_breaking_point[atoms] = met
......@@ -757,36 +881,52 @@ def ligands_and_metal_clusters(ase_atom):
for oxy in oxygen:
metal = [i for i in graph[oxy]
if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
if len(metal) > 0:
for met in metal:
bonds_to_break.append([oxy] + [met])
atom_pairs_at_breaking_point[oxy] = met
if ase_atom[atoms].symbol == 'N':
if atoms in list(all_sulfides.keys()):
sulphure = all_sulfides[atoms]
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
if len(metal) > 0 and atoms not in porphyrin_checker:
for met in metal:
bonds_to_break.append([atoms, met])
atom_pairs_at_breaking_point[atoms] = met
for sulf in sulphure:
metal = [i for i in graph[sulf]
if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
if len(metal) > 0:
for met in metal:
bonds_to_break.append([sulf, met])
atom_pairs_at_breaking_point[sulf] = met
if ase_atom[atoms].symbol == 'N':
if atoms not in porphyrin_checker:
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
if len(metal) > 0 and atoms not in porphyrin_checker:
for met in metal:
bonds_to_break.append([atoms, met])
atom_pairs_at_breaking_point[atoms] = met
# atom_pairs_at_breaking_point [metal[0]] = atoms
if ase_atom[atoms].symbol == 'S':
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
if len(metal) > 0:
if atoms not in seen_sulphure:
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
if len(metal) > 0:
for met in metal:
bonds_to_break.append([atoms] + [met])
atom_pairs_at_breaking_point[atoms] = met
if ase_atom[atoms].symbol == 'O':
# if not atoms in Seen_oxygen:
connected = graph[atoms]
metal = [
i for i in connected if ase_atom[i].symbol in transition_metals()]
metal = [i for i in metal if i not in porphyrin_checker]
Nitrogen = [i for i in connected if ase_atom[i].symbol == 'N']
carbon = [i for i in connected if ase_atom[i].symbol == 'C']
if len(metal) > 0 and len(carbon) == 1:
......@@ -811,18 +951,20 @@ def ligands_and_metal_clusters(ase_atom):
'''
Find the carbon closest to P, which is not bonded to a metal and cut
'''
connected = [i for i in graph[atoms]
if ase_atom[i].symbol not in transition_metals()]
metal_oxy = [[i for i in graph[j] if ase_atom[i].symbol in transition_metals()]
for j in connected]
metal = sum(metal_oxy, [])
closest_atoms = sum([[[i, j] for i in graph[j] if i != atoms and ase_atom[i].symbol in
transition_metals()]for j in connected], [])
for frag in closest_atoms:
bonds_to_break.append(frag)
atom_pairs_at_breaking_point[frag[0]] = frag[1]
if atoms not in list(all_phosphates.keys()):
connected = [i for i in graph[atoms]
if ase_atom[i].symbol not in transition_metals()]
metal_oxy = [[i for i in graph[j] if ase_atom[i].symbol in transition_metals()]
for j in connected]
metal = sum(metal_oxy, [])
metal = [i for i in metal if i not in porphyrin_checker]
closest_atoms = sum([[[i, j] for i in graph[j] if i != atoms and ase_atom[i].symbol in
transition_metals()]for j in connected], [])
for frag in closest_atoms:
bonds_to_break.append(frag)
atom_pairs_at_breaking_point[frag[0]] = frag[1]
for bonds in bonds_to_break:
bond_matrix[bonds[0], bonds[1]] = 0
......
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