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add function to handle fractional coordinates in lammps dump file #1

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Merged
amcadmus merged 1 commit into from
Jun 4, 2019
Merged

add function to handle fractional coordinates in lammps dump file #1

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28 changes: 26 additions & 2 deletions dpdata/lammps/dump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,30 @@ def get_posi(lines) :
posis = np.array(posis)
return posis[:,1:4]

def get_posi_frac(lines) :
blk, head = _get_block(lines, 'ATOMS')
keys = head.split()
id_idx = keys.index('id') - 2
xidx = keys.index('xs') - 2
yidx = keys.index('ys') - 2
zidx = keys.index('zs') - 2
sel = (xidx, yidx, zidx)
posis = []
for ii in blk :
words = ii.split()
posis.append([float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])])
posis.sort()
posis = np.array(posis)
return posis[:,1:4]

def safe_get_posi(lines, cell):
try:
posis = get_posi(lines)
except ValueError:
fposis = get_posi_frac(lines)
posis = fposis @ cell
return posis

def get_dumpbox(lines) :
blk, h = _get_block(lines, 'BOX BOUNDS')
bounds = np.zeros([3,2])
Expand Down Expand Up @@ -149,12 +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'] = [get_posi(lines) - 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(get_posi(array_lines[ii]) - np.array(orig))
system['coords'].append(safe_get_posi(lines, cell) - np.array(orig))
system['cells'] = np.array(system['cells'])
system['coords'] = np.array(system['coords'])
return system
Expand Down