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dpdata label system read ase db file #115
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726a86b
dpdata label system read ase db file
jwz360 1eba778
fix forces resort index
jwz360 dbe9ef3
start test ase db
jwz360 7381600
start test ase db
jwz360 a7f5811
fix atoms's sequence
jwz360 cab15e4
Merge branch 'master' of https://github.com/jwz360/dpdata
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,42 @@ | ||
from ase import Atom | ||
from ase.db import connect | ||
import numpy as np | ||
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def get_frames(fname, begin=0, step=1): | ||
asedb = connect(fname) | ||
num = asedb.count() | ||
at0 = asedb.get(1).toatoms() | ||
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numbers = at0.numbers | ||
nat0 = at0[numbers.argsort()] | ||
chemical_symbols = nat0.get_chemical_symbols() | ||
unique_numbers = np.unique(numbers) | ||
unique_numbers.sort() | ||
atom_names = [Atom(u).symbol for u in unique_numbers] | ||
atom_numbs = [chemical_symbols.count(i) for i in atom_names] | ||
atom_types = np.array([atom_names.index(i) for i in chemical_symbols]) | ||
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all_coords = [] | ||
all_cells = [] | ||
all_energies = [] | ||
all_forces = [] | ||
all_virials = None | ||
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for i in range(begin, num, step): | ||
ati = asedb.get(i+1) | ||
ats_ = ati.toatoms() | ||
numbers = ats_.numbers | ||
sorted_numbers = numbers.argsort() | ||
ats = ats_[sorted_numbers] | ||
data = ati.data | ||
energy = data['energy'] | ||
cell = ats.get_cell().view() | ||
coord = ats.positions | ||
forces = data['forces'][sorted_numbers] | ||
all_coords.append(coord) | ||
all_cells.append(cell) | ||
all_forces.append(forces) | ||
all_energies.append(energy) | ||
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return atom_names, atom_numbs, atom_types, np.array(all_cells), np.array(all_coords), np.array(all_energies), np.array(all_forces), all_virials |
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You need to use another directory name instead of
ase
, otherwise it will be conflict with thease
package when you importase
package in this directory.