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element.xu mode is added and displacement is forced to [-0.5,0.5] assuming… #124

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element.xu mode is added and displacement is forced to [-0.5,0.5] assuming… #124

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48 changes: 35 additions & 13 deletions tools/interface/LAMMPS.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,16 @@ def _print_displacements_and_forces(self, lammps_files, file_offset):

for idata in range(ndata):
disp = x[idata, :, :] - self._x_cartesian - disp_offset
if True:
# force disp vector the small magnitude assuming that the displacement is small.
# change displacemeent to the fractional coordinate
_disp_fracx = self._get_fractional_coordinate(disp, self._inverse_lattice_vector)
# make _fracx in [-0.5,0.5).
_disp_fracx += 0.5
_disp_fracx %= 1 # returns positive fractional part.. [0,1).
_disp_fracx -= 0.5 # adjust the center again
# convert to the cartedian coordinate again
disp = np.dot(_disp_fracx, self._lattice_vector.transpose())
disp *= self._disp_conversion_factor
f = force[idata, :, :] - force_offset
f *= self._force_conversion_factor
Expand Down Expand Up @@ -343,7 +353,7 @@ def _set_unit_conversion_factor(self, str_unit):

def _set_output_flags(self, output_flags):
self._print_disp, self._print_force, \
self._print_energy, self._print_born = output_flags
self._print_energy, self._print_born = output_flags

def _set_number_of_zerofill(self, npattern):

Expand Down Expand Up @@ -380,25 +390,37 @@ def x_fractional(self):
@staticmethod
def _get_coordinate_and_force_lammps(lammps_dump_file):

add_flag = False
add_flag = None
ret = []

with open(lammps_dump_file) as f:
for line in f:
if "ITEM:" in line and "ITEM: ATOMS id xu yu zu fx fy fz" not in line:
add_flag = False
# if "ITEM:" in line and "ITEM: ATOMS id xu yu zu fx fy fz" not in line:
# add_flag = False
# continue
if "ITEM: ATOMS id xu yu zu fx fy fz" in line:
add_flag = "id.xu"
continue
elif "ITEM: ATOMS id xu yu zu fx fy fz" in line:
add_flag = True
elif "ITEM: ATOMS element xu yu zu fx fy fz" in line:
add_flag = "element.xu"
id_ = 0
continue

if add_flag:
if line.strip():
entries = line.strip().split()
data_atom = [int(entries[0]),
[float(t) for t in entries[1:4]],
[float(t) for t in entries[4:]]]

if add_flag is not None:
if add_flag == "id.xu":
if line.strip():
entries = line.strip().split()
data_atom = [int(entries[0]),
[float(t) for t in entries[1:4]],
[float(t) for t in entries[4:]]]
ret.append(data_atom)
elif add_flag == "element.xu":
if line.strip():
entries = line.strip().split()
id_ += 1
data_atom = [int(id_),
[float(t) for t in entries[1:4]],
[float(t) for t in entries[4:]]]
ret.append(data_atom)

# This sort is necessary since the order atoms of LAMMPS dump files
Expand Down