def main(argv=None):
if argv is None:
argv = sys.argv
argc = len(argv)
self = "link.py"
if argv[0][-len(self) :] != self:
sys.exit("\n Rename script to %s\n" % self)
if argc != 15:
sys.exit(
"\n Usage: %s fnc ffc fns ffs fna ffa icb icd isb isd acs facs rcs frcs\n" % self
+ " Description: links the side chain read from file fns to the core structure\n"
+ " read from file fnc and writes the obtained adduct to file fna. Variables\n"
+ " ffc, ffs, ffa set to mat|paratec|vasp|espresso|siesta|tbpw|xyz|xsf specify\n"
+ " the file formats. The core and side atoms with indices icb and isb are\n"
+ " bonded together, while the core and side atoms with indices icd and isd\n"
+ " are detached. The side chain is oriented in such a way that bonds icb-icd,\n"
+ " isd-isb, and icb-isb are all collinear. Variable acs gives the angle by\n"
+ " which the side chain is rotated around the icb-isb axis. Variable rcs\n"
+ " gives the distance between icb and isb atoms. Variables facs and frcs set\n"
+ " to radian or degree and bohr or angstrom define the units of acs and rcs.\n"
)
fnc = argv[1]
ffc = argv[2].lower()
fns = argv[3]
ffs = argv[4].lower()
fna = argv[5]
ffa = argv[6].lower()
try:
icb = int(argv[7]) - 1
except:
icb = -1
try:
icd = int(argv[8]) - 1
except:
icd = -1
try:
isb = int(argv[9]) - 1
except:
isb = -1
try:
isd = int(argv[10]) - 1
except:
isd = -1
try:
acs = float(argv[11])
except:
sys.exit("\n Error: acs %s\n" % argv[11])
facs = argv[12].lower()
if facs == "r" or facs == "rad" or facs == "radian":
pass
elif facs == "d" or facs == "deg" or facs == "degree":
acs *= math.pi / 180.0
else:
sys.exit("\n Error: facs %s\n" % argv[12])
try:
rcs = float(argv[13])
except:
rsc = -inf9
if rcs < eps9:
sys.exit("\n Error: rcs %s\n" % argv[13])
frcs = argv[14].lower()
if frcs == "b" or frcs == "bohr":
format = format_index2mat[0]
elif frcs == "a" or frcs == "ang" or frcs == "angstrom":
format = format_index2mat[1]
else:
sys.exit("\n Error: frcs %s\n" % argv[14])
if ffc == "mat":
ierr, matc = mat_read(fnc)
elif ffc == "paratec":
ierr, matc = paratec_read(fnc)
elif ffc == "vasp":
ierr, matc = vasp_read(fnc)
elif ffc == "espresso":
ierr, matc = espresso_read(fnc)
elif ffc == "siesta":
ierr, matc = siesta_read(fnc)
elif ffc == "tbpw":
ierr, matc = tbpw_read(fnc)
elif ffc == "xyz":
ierr, matc = xyz_read(fnc)
elif ffc == "xsf":
ierr, matc = xsf_read(fnc)
else:
sys.exit("\n Error: invalid input format %s\n" % ffc)
if ierr != 0:
sys.exit("\n Error: unable to read file %s\n" % fnc)
ierr = mat_check(matc)
if ierr != 0:
sys.exit("\n Error: invalid content in file %s\n" % fnc)
matc = mat_format(matc, format, format, format, format)
if matc["fc"] != format or matc["fo"] != format or matc["fv"] != format or matc["fp"] != format:
sys.exit("\n Error: unable to change format in file %s\n" % fnc)
if icb < 0 or icb > matc["na"] - 1:
sys.exit("\n Error: icb %s\n" % argv[7])
if icd < 0 or icd > matc["na"] - 1 or icd == icb:
sys.exit("\n Error: icd %s\n" % argv[8])
vc = []
for j in range(3):
vc.append(matc["ap"][icd][j] - matc["ap"][icb][j])
rc = 0.0
for j in range(3):
rc += math.pow(vc[j], 2)
rc = math.sqrt(rc)
if rc < eps9:
sys.exit("\n Error: atomic positions in file %s\n" % fnc)
if ffs == "mat":
ierr, mats = mat_read(fns)
elif ffs == "paratec":
ierr, mats = paratec_read(fns)
elif ffs == "vasp":
ierr, mats = vasp_read(fns)
elif ffs == "espresso":
ierr, mats = espresso_read(fns)
elif ffs == "siesta":
ierr, mats = siesta_read(fns)
elif ffs == "tbpw":
ierr, mats = tbpw_read(fns)
elif ffs == "xyz":
ierr, mats = xyz_read(fns)
elif ffs == "xsf":
ierr, mats = xsf_read(fns)
else:
sys.exit("\n Error: invalid input format %s\n" % ffs)
if ierr != 0:
sys.exit("\n Error: unable to read file %s\n" % fns)
ierr = mat_check(matc)
if ierr != 0:
sys.exit("\n Error: invalid content in file %s\n" % fns)
mats = mat_format(mats, format, format, format, format)
if mats["fc"] != format or mats["fo"] != format or mats["fv"] != format or mats["fp"] != format:
sys.exit("\n Error: unable to change format in file %s\n" % fns)
if isb < 0 or isb > mats["na"] - 1:
sys.exit("\n Error: isb %s\n" % argv[9])
if isd < 0 or isd > mats["na"] - 1 or isd == isb:
sys.exit("\n Error: isd %s\n" % argv[10])
vs = []
for j in range(3):
vs.append(mats["ap"][isb][j] - mats["ap"][isd][j])
rs = 0.0
for j in range(3):
rs += math.pow(vs[j], 2)
rs = math.sqrt(rs)
if rs < eps9:
sys.exit("\n Error: atomic positions in file %s\n" % fns)
numberc, axesc, anglesc = align_vector(vc)
numbers, axess, angless = align_vector(vs)
number = numbers + 1 + numberc
axes = []
angles = []
for i in range(numbers):
axes.append(axess[i])
angles.append(angless[i])
axes.append(2)
angles.append(acs)
for i in range(numberc - 1, -1, -1):
axes.append(axesc[i])
angles.append(-anglesc[i])
rotation = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
for i in range(number):
rotation = matrix_dot_matrix(rotation_matrix(axes[i], angles[i]), rotation)
mats = mat_rotate(mats, rotation)
translation = [0.0, 0.0, 0.0]
for j in range(3):
translation[j] += matc["ap"][icb][j] - mats["ap"][isb][j] + vc[j] * rcs / rc
mats = mat_translate(mats, translation, format)
matc = mat_remove(matc, icd)
mats = mat_remove(mats, isd)
mata = mat_merge(matc, mats)
if ffa == "mat":
ierr = mat_write(fna, mata)
elif ffa == "paratec":
ierr = paratec_write(fna, mata)
elif ffa == "vasp":
ierr = vasp_write(fna, mata)
elif ffa == "espresso":
ierr = espresso_write(fna, mata)
elif ffa == "siesta":
ierr = siesta_write(fna, mata)
elif ffa == "tbpw":
ierr = tbpw_write(fna, mata)
elif ffa == "xyz":
ierr = xyz_write(fna, mata)
elif ffa == "xsf":
ierr = xsf_write(fna, mata)
else:
sys.exit("\n Error: invalid output format %s\n" % ffa)
if ierr != 0:
sys.exit("\n Error: unable to write file %s\n" % fna)
return 0
def main(argv = None):
if argv is None:
argv = sys.argv
argc = len(argv)
self = "convert.py"
if argv[0][-len(self):] != self:
sys.exit("\n Rename script to %s\n" % self)
if not (argc == 5 or (argc > 5 and ((argv[5].lower() == 'units' and argc == 9) or (argv[5].lower() == 'vacuum' and argc == 9) or (argv[5].lower() == 'supercell' and (argc == 7 or argc == 20)) or (argv[5].lower() == 'translate' and argc == 10) or (argv[5].lower() == 'rotate' and (argc == 8 or argc == 9)) or (argv[5].lower() == 'center' and argc == 8) or (argv[5].lower() == 'minbox' and argc == 7)))):
sys.exit("\n Usage: %s ifn iff ofn off [action parameters]\n" % self +
" ifn = input file name ofn = output file name\n" +
" iff = input file format off = output file format\n" +
" format = mat|paratec|vasp|espresso|siesta|tbpw|xyz|xsf|wien|povray\n" +
" (wien & povray are only for output)\n\n" +
" action parameters\n" +
" ------------------\n" +
" units lattice_constant_units lattice_vector_units atomic_position_units\n" +
" vacuum axes separation_distance separation_distance_units\n" +
" supercell ( sc_file | sc_origin sc_vectors sc_units sc_translation )\n" +
" translate translation_vector translation_vector_units\n" +
" rotate axis ( rotation_angle | adjacent_side opposite_side )\n" +
" center axes center_type\n" +
" minbox axes\n\n" +
" axis = x | y | z rotation_angle in degrees\n" +
" axes = x & y & z *_side in arbitrary cartesian units\n" +
" sc_translation = true | false center_type = geometric | mass\n" +
" *_units = bohr | angstrom | latconst | latvec\n")
ifn = argv[1]
ift = argv[2].lower()
ofn = argv[3]
oft = argv[4].lower()
if ift == 'mat':
ierr, mat = mat_read(ifn)
elif ift == 'paratec':
ierr, mat = paratec_read(ifn)
elif ift == 'vasp':
ierr, mat = vasp_read(ifn)
elif ift == 'espresso':
ierr, mat = espresso_read(ifn)
elif ift == 'siesta':
ierr, mat = siesta_read(ifn)
elif ift == 'tbpw':
ierr, mat = tbpw_read(ifn)
elif ift == 'xyz':
ierr, mat = xyz_read(ifn)
elif ift == 'xsf':
ierr, mat = xsf_read(ifn)
else:
sys.exit("\n Error: invalid input format %s\n" % ift)
if ierr != 0:
sys.exit("\n Error: unable to read file %s\n" % ifn)
ierr = mat_check(mat)
if ierr != 0:
sys.exit("\n Error: invalid content in file %s\n" % ifn)
if oft == 'povray':
st = 1
umat = {}
smin = []
smax = []
si = []
if argc != 5:
if argv[5].lower() == 'units':
ierr, fc = format_input(argv[6], 2)
if ierr != 0:
sys.exit("\n Error: invalid lattice_constant_units %s\n" % argv[6])
ierr, fo = format_input(argv[7], 3)
if ierr != 0:
sys.exit("\n Error: invalid lattice_vector_units %s\n" % argv[7])
ierr, fp = format_input(argv[8], 4)
if ierr != 0:
sys.exit("\n Error: invalid atomic_position_units %s\n" % argv[8])
if fo == format_index2mat[3]:
fv = format_index2mat[2]
else:
fv = fo
mat = mat_format(mat, fc, fo, fv, fp)
elif argv[5].lower() == 'vacuum':
axes = axes_input(argv[6])
try:
distance = float(argv[7])
except:
sys.exit("\n Error: invalid separation_distance %s\n" % argv[7])
ierr, format = format_input(argv[8], 3)
if ierr != 0:
sys.exit("\n Error: invalid separation_distance_units %s\n" % argv[8])
mat = mat_lattice(mat, axes, distance, format)
elif argv[5].lower() == 'supercell':
if argc == 7:
ierr = 0
try:
h = open(argv[6], 'r')
except:
ierr = 1
if ierr == 0:
r = h.readlines()
h.close()
s = r[0]
t = s.split()
so = [float(t[0]), float(t[1]), float(t[2])]
sv = []
for i in range(3):
s = r[i + 1]
t = s.split()
sv.append([float(t[0]), float(t[1]), float(t[2])])
s = r[4]
t = s.split()
jerr, format = format_input(t[0], 4)
ierr += jerr
s = r[5]
t = s.split()
jerr, st = boolean_input(t[0])
ierr += jerr
if ierr != 0:
sys.exit("\n Error: unable to read supercell_file %s\n" % argv[6])
else:
try:
so = [float(argv[6]), float(argv[7]), float(argv[8])]
except:
sys.exit("\n Error: invalid supercell_origin %s %s %s\n" % (argv[6], argv[7], argv[8]))
try:
sv = [[float(argv[9]), float(argv[10]), float(argv[11])], [float(argv[12]), float(argv[13]), float(argv[14])], [float(argv[15]), float(argv[16]), float(argv[17])]]
except:
sys.exit("\n Error: invalid supercell_vectors %s %s %s %s %s %s %s %s %s\n" % (argv[9], argv[10], argv[11], argv[12], argv[13], argv[14], argv[15], argv[16], argv[17]))
ierr, format = format_input(argv[18], 4)
if ierr != 0:
sys.exit("\n Error: invalid supercell_units %s\n" % argv[18])
ierr, st = boolean_input(argv[19])
if ierr != 0:
sys.exit("\n Error: invalid supercell_translation %s\n" % argv[19])
if st == 0:
umat = copy.deepcopy(mat)
smin, smax, si, mat = mat_replicate(mat, so, sv, format)
elif argv[5].lower() == 'translate':
try:
translation = [float(argv[6]), float(argv[7]), float(argv[8])]
except:
sys.exit("\n Error: invalid translation_vector %s %s %s\n" % (argv[6], argv[7], argv[8]))
ierr, format = format_input(argv[9], 4)
if ierr != 0:
sys.exit("\n Error: invalid translation_vector_units %s\n" % argv[9])
mat = mat_translate(mat, translation, format)
elif argv[5].lower() == 'rotate':
ierr, axis = axis_input(argv[6])
if argc == 8:
try:
angle = float(argv[7]) * math.pi / 180.0
except:
sys.exit("\n Error: invalid rotation_angle %s\n" % argv[7])
else:
try:
adjacent = float(argv[7])
except:
sys.exit("\n Error: invalid adjacent_side %s\n" % argv[7])
try:
opposite = float(argv[8])
except:
sys.exit("\n Error: invalid opposite_side %s\n" % argv[8])
angle = math.atan2(opposite, adjacent)
rotation = rotation_matrix(axis, angle)
mat = mat_rotate(mat, rotation)
elif argv[5].lower() == 'center':
axes = axes_input(argv[6])
ierr, center_type = center_input(argv[7])
if ierr != 0:
sys.exit("\n Error: invalid center_type %s\n" % argv[7])
format = mat['fp']
center = []
if center_type == 0:
fr, rmin, rmax = mat_range(mat['na'], mat['fc'], mat['lc'], mat['fv'], mat['lv'], mat['fp'], mat['ap'], format)
if fr != format:
sys.exit("\n Error: failed center_type geometric\n")
for j in range(3):
center.append((rmin[j] + rmax[j]) / 2)
else:
if format == format_index2mat[3]:
sys.exit("\n Error: center_type mass incompatible with atomic_position_units %s\n" % format)
total_mass = 0.0
for j in range(3):
center.append(0.0)
for i in range(mat['na']):
atomic_mass = periodic_table[index_by_number(mat['as'][i])]['mass']
total_mass += atomic_mass
for j in range(3):
center[j] += mat['ap'][i][j] * atomic_mass
if abs(total_mass) > eps9:
for j in range(3):
center[j] /= total_mass
else:
sys.exit("\n Error: failed center_type mass\n")
translation = []
for j in range(3):
translation.append(-center[j] * axes[j])
mat = mat_translate(mat, translation, format)
elif argv[5].lower() == 'minbox':
axes = axes_input(argv[6])
for i in range(3):
if axes[i] == 1:
for j in range(3):
if j != i:
minwidth = inf9
minangle = 0.0
for k in range(180):
angle = float(k) * math.pi / 180.0
rotation = rotation_matrix(j, angle)
cmat = copy.deepcopy(mat)
rmat = mat_rotate(cmat, rotation)
format, rmin, rmax = mat_range(rmat['na'], rmat['fc'], rmat['lc'], rmat['fv'], rmat['lv'], rmat['fp'], rmat['ap'], 'bohr')
cmat = []
rmat = []
width = rmax[i] - rmin[i]
if width < minwidth - eps9:
minwidth = width
minangle = angle
rotation = rotation_matrix(j, minangle)
cmat = copy.deepcopy(mat)
mat = mat_rotate(cmat, rotation)
cmat = []
if oft == 'povray':
box = 1
basis = 1
if st != 0:
ierr, bonds = povray_bonds_st(mat)
else:
ierr, bonds = povray_bonds_ut(mat, umat, smin, smax, si)
if ierr != 0:
sys.exit("\n Error: failed povray_bonds\n")
if oft == 'mat':
ierr = mat_write(ofn, mat)
elif oft == 'paratec':
ierr = paratec_write(ofn, mat)
elif oft == 'vasp':
ierr = vasp_write(ofn, mat)
elif oft == 'espresso':
ierr = espresso_write(ofn, mat)
elif oft == 'siesta':
ierr = siesta_write(ofn, mat)
elif oft == 'tbpw':
ierr = tbpw_write(ofn, mat)
elif oft == 'xyz':
ierr = xyz_write(ofn, mat)
elif oft == 'xsf':
ierr = xsf_write(ofn, mat)
elif oft == 'wien':
ierr = wien_write(ofn, mat)
elif oft == 'povray':
ierr = povray_write(ofn, mat, box, basis, bonds)
else:
sys.exit("\n Error: invalid output format %s\n" % oft)
if ierr != 0:
sys.exit("\n Error: unable to write file %s\n" % ofn)
return 0