def dumpbox2box(bounds, tilt):
xy = tilt[0]
xz = tilt[1]
yz = tilt[2]
xlo = bounds[0][0] - min(0.0, xy, xz, xy + xz)
xhi = bounds[0][1] - max(0.0, xy, xz, xy + xz)
ylo = bounds[1][0] - min(0.0, yz)
yhi = bounds[1][1] - max(0.0, yz)
zlo = bounds[2][0]
zhi = bounds[2][1]
info = [[xlo, xhi], [ylo, yhi], [zlo, zhi]]
return lmp.lmpbox2box(info, tilt)
def add_bonds (lines_, max_roh = 1.3) :
lines = lines_
natoms = lmp.get_natoms_vec(lines)
assert(len(natoms) == 2)
# type 1 == O, type 2 == H
assert(natoms[0] == natoms[1] // 2)
atype = lmp.get_atype(lines)
posis = lmp.get_posi(lines)
bounds, tilt = lmp.get_lmpbox(lines)
orig, box = lmp.lmpbox2box(bounds, tilt)
bonds = compute_bonds(box, atype, posis, max_roh)
# check water moles
for ii in range(len(bonds)) :
if atype[ii] == 1 :
assert(len(bonds[ii]) == 2), 'ill defined O atom %d has H %s' % (ii, bonds[ii])
elif atype[ii] == 2 :
assert(len(bonds[ii]) == 1), 'ill defined H atom %d has O %s' % (ii, bonds[ii])
# pbc posi
for ii in range(sum(natoms)) :
if atype[ii] == 1:
j0idx = bonds[ii][0]
shift0 = posi_shift(box, posis[j0idx], posis[ii])
posis[j0idx] = posis[j0idx] + np.dot(box.T, shift0)
j1idx = bonds[ii][1]
shift1 = posi_shift(box, posis[j1idx], posis[ii])
posis[j1idx] = posis[j1idx] + np.dot(box.T, shift1)
for atoms_idx in range(len(lines)) :
if 'Atoms' in lines[atoms_idx] :
break
for ii in range(sum(natoms)) :
words = lines[atoms_idx + 2 +ii].split()
words[2] = str(posis[ii][0])
words[3] = str(posis[ii][1])
words[4] = str(posis[ii][2])
lines[atoms_idx+2+ii] = ' '.join(words)
ret_bd = []
idx = 1
for ii in range(len(bonds)) :
if atype[ii] == 1:
ret_bd.append("%d 1 %d %d" % (idx, 1+ii, 1+bonds[ii][0]))
idx += 1
ret_bd.append("%d 1 %d %d" % (idx, 1+ii, 1+bonds[ii][1]))
idx += 1
ret_ang = []
idx = 1
for ii in range(len(bonds)) :
if atype[ii] == 1:
ret_ang.append("%d 1 %d %d %d" % (idx, 1+bonds[ii][0], 1+ii, 1+bonds[ii][1]))
idx += 1
lines.append('Bonds')
lines.append('')
lines += ret_bd
lines.append('')
lines.append('Angles')
lines.append('')
lines += ret_ang
lines.append('')
lines.append('')
nbonds = len(ret_bd)
nangles = len(ret_ang)
for atoms_idx in range(len(lines)) :
if 'atoms' in lines[atoms_idx] :
break
lines.insert(atoms_idx+1, '%d angles' % nangles)
lines.insert(atoms_idx+1, '%d bonds' % nbonds)
for atoms_types_idx in range(len(lines)) :
if 'atom types' in lines[atoms_types_idx] :
break
lines.insert(atoms_types_idx+1, '%d angle types' % 1)
lines.insert(atoms_types_idx+1, '%d bond types' % 1)
for atoms_idx in range(len(lines)) :
if 'Atoms' in lines[atoms_idx] :
break
mole_idx = np.zeros(sum(natoms), dtype = int)
cc = 1
for ii in range(sum(natoms)) :
if atype[ii] == 1 :
mole_idx[ii] = cc
cc += 1
for ii in range(sum(natoms)) :
if atype[ii] == 2 :
mole_idx[ii] = mole_idx[bonds[ii]]
cc = 0
for idx in range(atoms_idx+2, atoms_idx+2+sum(natoms)) :
words = lines[idx].split()
words.insert(1, '%d' % mole_idx[cc])
lines[idx] = ' '.join(words)
cc += 1
return lines
return list_oh
def dist_via_oh_list(box, posis, list_oh) :
dist = []
for ii in list_oh :
dij = np.linalg.norm(posi_diff(box, posis[ii[0]], posis[ii[1]]))
dist.append(dij)
return dist
if __name__ == '__main__' :
fname = 'conf.lmp'
lines = open(fname).read().split('\n')
# lines = add_bonds(lines)
# print('\n'.join(ret_bd))
# print('\n'.join(ret_ang))
atype = lmp.get_atype(lines)
posis = lmp.get_posi(lines)
bounds, tilt = lmp.get_lmpbox(lines)
orig, box = lmp.lmpbox2box(bounds, tilt)
# md_oo = min_oo(box, atype, posis)
# md_ho = min_ho(box, atype, posis)
# print(np.average(md_oo), np.average(md_ho), np.min(md_ho), np.max(md_ho))
moh, moh2, moo = min_oho(box, atype, posis)
print(np.max(moh), np.average(moh2), np.average(moo))