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Merged
wanghan-iapcm merged 3 commits into from
Jun 22, 2023
Merged

Use stable sorting algorithms #487

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d528cfa
use stable sort
njzjz Jun 21, 2023
2ecc207
replace the test case
njzjz Jun 21, 2023
e883db3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 21, 2023
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2 changes: 1 addition & 1 deletion dpdata/cp2k/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -494,7 +494,7 @@ def get_frames(fname):
atom_types = []
atom_numbs = []
# preserve the atom_name order
atom_names = atom_symbol_list[np.sort(symbol_idx)]
atom_names = atom_symbol_list[np.sort(symbol_idx, kind="stable")]
for jj in atom_symbol_list:
for idx, ii in enumerate(atom_names):
if jj == ii:
Expand Down
4 changes: 3 additions & 1 deletion dpdata/lammps/dump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,9 @@ def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False):
system["cells"].append(cell)
atype = get_atype(array_lines[ii], type_idx_zero=type_idx_zero)
# map atom type; a[as[a][as[as[b]]]] = b[as[b][as^{-1}[b]]] = b[id]
idx = np.argsort(atype)[np.argsort(np.argsort(system["atom_types"]))]
idx = np.argsort(atype, kind="stable")[
np.argsort(np.argsort(system["atom_types"], kind="stable"), kind="stable")
]
system["coords"].append(
safe_get_posi(array_lines[ii], cell, np.array(orig), unwrap)[idx]
)
Expand Down
2 changes: 1 addition & 1 deletion dpdata/md/rdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ def compute_rdf(box, posis, atype, sel_type=[None, None], max_r=5, nbins=100):


def _compute_rdf_1frame(box, posis, atype, sel_type=[None, None], max_r=5, nbins=100):
all_types = list(set(list(np.sort(atype))))
all_types = list(set(list(np.sort(atype, kind="stable"))))
if sel_type[0] is None:
sel_type[0] = all_types
if sel_type[1] is None:
Expand Down
2 changes: 1 addition & 1 deletion dpdata/qe/scf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ def get_coords(lines, cell):
atom_types = []
atom_numbs = []
# preserve the atom_name order
atom_names = atom_symbol_list[np.sort(symbol_idx)]
atom_names = atom_symbol_list[np.sort(symbol_idx, kind="stable")]
for jj in atom_symbol_list:
for idx, ii in enumerate(atom_names):
if jj == ii:
Expand Down
4 changes: 2 additions & 2 deletions dpdata/system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -624,7 +624,7 @@ def sort_atom_types(self) -> np.ndarray:
idx : np.ndarray
new atom index in the Axis.NATOMS
"""
idx = np.argsort(self.data["atom_types"])
idx = np.argsort(self.data["atom_types"], kind="stable")
for tt in self.DTYPES:
if tt.name not in self.data:
# skip optional data
Expand Down Expand Up @@ -767,7 +767,7 @@ def replicate(self, ncopy):
np.array(np.copy(data["atom_numbs"])) * np.prod(ncopy)
)
tmp.data["atom_types"] = np.sort(
np.tile(np.copy(data["atom_types"]), np.prod(ncopy))
np.tile(np.copy(data["atom_types"]), np.prod(ncopy)), kind="stable"
)
tmp.data["cells"] = np.copy(data["cells"])
for ii in range(3):
Expand Down
8 changes: 5 additions & 3 deletions dpdata/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,14 +63,16 @@ def sort_atom_names(data, type_map=None):
# a[as[a]] == b[as[b]] as == argsort
# as[as[b]] == as^{-1}[b]
# a[as[a][as[as[b]]]] = b[as[b][as^{-1}[b]]] = b[id]
idx = np.argsort(data["atom_names"])[np.argsort(np.argsort(type_map))]
idx = np.argsort(data["atom_names"], kind="stable")[
np.argsort(np.argsort(type_map, kind="stable"), kind="stable")
]
else:
# index that will sort an array by alphabetical order
idx = np.argsort(data["atom_names"])
idx = np.argsort(data["atom_names"], kind="stable")
# sort atom_names, atom_numbs, atom_types by idx
data["atom_names"] = list(np.array(data["atom_names"])[idx])
data["atom_numbs"] = list(np.array(data["atom_numbs"])[idx])
data["atom_types"] = np.argsort(idx)[data["atom_types"]]
data["atom_types"] = np.argsort(idx, kind="stable")[data["atom_types"]]
return data


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192 changes: 96 additions & 96 deletions tests/poscars/POSCAR.P42nmc.replace
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Original file line number Diff line number Diff line change
Expand Up @@ -6,99 +6,99 @@ Hf24 O64 Zr8
Hf O Zr
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