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fix bug in lammps/dump, fractional coord should not shift origin #96

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Merged
amcadmus merged 2 commits into from
Apr 16, 2020
Merged

fix bug in lammps/dump, fractional coord should not shift origin #96

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207ffde
fix bug in lammps/dump, fractional coord should not shift origin
Apr 16, 2020
a9e726a
fix bug in lammps/dump
Apr 16, 2020
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8 changes: 4 additions & 4 deletions dpdata/lammps/dump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,9 +83,9 @@ def get_posi_frac(lines) :
posis = np.array(posis)
return posis[:,1:4]

def safe_get_posi(lines, cell):
def safe_get_posi(lines, cell, orig = np.zeros(3)):
try:
posis = get_posi(lines)
posis = get_posi(lines) - orig
except ValueError:
fposis = get_posi_frac(lines)
posis = fposis @ cell
Expand Down Expand Up @@ -173,12 +173,12 @@ def system_data(lines, type_map = None, type_idx_zero = True) :
system['cells'] = [np.array(cell)]
natoms = sum(system['atom_numbs'])
system['atom_types'] = get_atype(lines, type_idx_zero = type_idx_zero)
system['coords'] = [safe_get_posi(lines, cell) - np.array(orig)]
system['coords'] = [safe_get_posi(lines, cell, np.array(orig))]
for ii in range(1, len(array_lines)) :
bounds, tilt = get_dumpbox(array_lines[ii])
orig, cell = dumpbox2box(bounds, tilt)
system['cells'].append(cell)
system['coords'].append(safe_get_posi(array_lines[ii], cell) - np.array(orig))
system['coords'].append(safe_get_posi(array_lines[ii], cell, np.array(orig)))
system['cells'] = np.array(system['cells'])
system['coords'] = np.array(system['coords'])
return system
Expand Down