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Sort atom according to the type_map in Multisystem #109

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Merged
amcadmus merged 4 commits into from
Aug 11, 2020
Merged

Sort atom according to the type_map in Multisystem #109

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13bd118
Merge pull request #2 from deepmodeling/devel
zezhong-zhang Aug 10, 2020
6c83ca8
sort atom according to the type_map of user input instead of alphabet…
zezhong-zhang Aug 10, 2020
ae7ff40
bug fix && modify set subtraction
felix5572 Aug 11, 2020
eb37843
Merge pull request #3 from felix5572/zezhong-devel
zezhong-zhang Aug 11, 2020
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19 changes: 11 additions & 8 deletions dpdata/system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -368,7 +368,8 @@ def sort_atom_names(self, type_map=None):
# atom_names must be a subset of type_map
assert (set(self.data['atom_names']).issubset(set(type_map)))
# for the condition that type_map is a proper superset of atom_names
new_atoms = set(type_map) - set(self.data["atom_names"])
# new_atoms = set(type_map) - set(self.data["atom_names"])
new_atoms = [e for e in type_map if e not in self.data["atom_names"]]
if new_atoms:
self.add_atom_names(new_atoms)
# index that will sort an array by type_map
Expand Down Expand Up @@ -414,8 +415,8 @@ def formula(self):
"""
Return the formula of this system, like C3H5O2
"""
return ''.join(["{}{}".format(symbol,numb) for symbol,numb in sorted(
zip(self.data['atom_names'], self.data['atom_numbs']))])
return ''.join(["{}{}".format(symbol,numb) for symbol,numb in
zip(self.data['atom_names'], self.data['atom_numbs'])])


def extend(self, systems):
Expand Down Expand Up @@ -1455,29 +1456,31 @@ def check_atom_names(self, system):
"""
Make atom_names in all systems equal, prevent inconsistent atom_types.
"""
new_in_system = set(system["atom_names"]) - set(self.atom_names)
new_in_self = set(self.atom_names) - set(system["atom_names"])
# new_in_system = set(system["atom_names"]) - set(self.atom_names)
# new_in_self = set(self.atom_names) - set(system["atom_names"])
new_in_system = [e for e in system["atom_names"] if e not in self.atom_names]
new_in_self = [e for e in self.atom_names if e not in system["atom_names"]]
if len(new_in_system):
# A new atom_name appear, add to self.atom_names
self.atom_names.extend(new_in_system)
self.atom_names.sort()

@njzjz njzjz Aug 10, 2020 •
edited
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I am wondering whether we need to sort atom names when self.atom_names does not have the enough elements?

# Add this atom_name to each system, and change their names
new_systems = {}
for each_system in self.systems.values():
each_system.add_atom_names(new_in_system)
each_system.sort_atom_names()
each_system.sort_atom_names(type_map=self.atom_names)
new_systems[each_system.formula] = each_system
self.systems = new_systems
if len(new_in_self):
# Previous atom_name not in this system
system.add_atom_names(new_in_self)
system.sort_atom_names()
system.sort_atom_names(type_map=self.atom_names)

def from_quip_gap_xyz_file(self,file_name):
# quip_gap_xyz_systems = QuipGapxyzSystems(file_name)
# print(next(quip_gap_xyz_systems))
for info_dict in QuipGapxyzSystems(file_name):
system=LabeledSystem(data=info_dict)
system.sort_atom_names()
self.append(system)


Expand Down