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
def main(argv = None):
if argv is None:
argv = sys.argv
argc = len(argv)
self = "gsphere.py"
if argv[0][-len(self):] != self:
sys.exit("\n Rename script to %s\n" % self)
if argc != 3:
sys.exit("\n Usage: %s ifn ofn\n" % self +
" Description: reads system info from file ifn, generates the G-space\n" +
" and writes it to file ofn. ifn contains: lattice vectors (in bohr),\n" +
" energy cutoff (in Ry), FFT grid (set to zero to determine automatically)\n" +
" flag (true or false) for sorting the G-vectors, and optionally a k- or\n" +
" q-point (reduced coords). The number of G-vectors is roughly equal to\n" +
" N = V * E^(3/2) / (6 * pi^2) where V is the volume of the unit cell\n" +
" (in bohr^3) and E is the energy cutoff (in Ry).\n")
ifn = argv[1]
ofn = argv[2]
ierr = 0
try:
h = open(ifn, 'r')
except:
ierr = 1
if ierr == 0:
a = []
for i in range(3):
a.append([])
s = h.readline()
t = s.split()
for j in range(3):
a[i].append(float(t[j]))
s = h.readline()
t = s.split()
ecut = float(t[0])
s = h.readline()
t = s.split()
nr = [int(t[0]), int(t[1]), int(t[2])]
s = h.readline()
t = s.split()
ierr, fsort = boolean_input(t[0])
try:
s = h.readline()
t = s.split()
kpt = [float(t[0]), float(t[1]), float(t[2])]
kpt_given = True
except:
kpt = [0.0, 0.0, 0.0]
kpt_given = False
h.close()
if ierr != 0:
sys.exit("\n Error: unable to read file %s\n" % ifn)
al = math.sqrt(a[0][0] * a[0][0] + a[0][1] * a[0][1] + a[0][2] * a[0][2])
for i in range(3):
for j in range(3):
a[i][j] /= al
vol = 0.0
vol += a[0][0] * (a[1][1] * a[2][2] - a[2][1] * a[1][2])
vol -= a[0][1] * (a[1][0] * a[2][2] - a[2][0] * a[1][2])
vol += a[0][2] * (a[1][0] * a[2][1] - a[2][0] * a[1][1])
bl = 2.0 * math.pi / al
b = [[], [], []]
b[0].append((a[1][1] * a[2][2] - a[1][2] * a[2][1]) / vol)
b[0].append((a[1][2] * a[2][0] - a[1][0] * a[2][2]) / vol)
b[0].append((a[1][0] * a[2][1] - a[1][1] * a[2][0]) / vol)
b[1].append((a[2][1] * a[0][2] - a[2][2] * a[0][1]) / vol)
b[1].append((a[2][2] * a[0][0] - a[2][0] * a[0][2]) / vol)
b[1].append((a[2][0] * a[0][1] - a[2][1] * a[0][0]) / vol)
b[2].append((a[0][1] * a[1][2] - a[0][2] * a[1][1]) / vol)
b[2].append((a[0][2] * a[1][0] - a[0][0] * a[1][2]) / vol)
b[2].append((a[0][0] * a[1][1] - a[0][1] * a[1][0]) / vol)
vol = abs(vol) * al * al * al
gcutm = ecut / (bl * bl)
try:
h = open(ofn, 'w')
except:
sys.exit("\n Error: unable to write file %s\n" % ofn)
h.write('\n')
for i in range(3):
s = ' a%1i =' % (i + 1)
for j in range(3):
s += ' %13.9f' % (al * a[i][j])
s += '\n'
h.write(s)
h.write('\n')
for i in range(3):
s = ' b%1i =' % (i + 1)
for j in range(3):
s += ' %13.9f' % (bl * b[i][j])
s += '\n'
h.write(s)
h.write('\n')
s = ' volume = %.9f\n' % vol
h.write(s)
h.write('\n')
s = ' cutoff = %.9f\n' % ecut
h.write(s)
h.write('\n')
if nr[0] < 1 or nr[1] < 1 or nr[2] < 1:
for i in range(3):
nr[i] = 2 * int(math.sqrt(gcutm) * math.sqrt(a[i][0] * a[i][0] + a[i][1] * a[i][1] + a[i][2] * a[i][2])) + 1
nr6 = []
for i in range(3):
nr6.append(nr[i])
while not check_nr_size(nr6[i], 6):
nr6[i] += 1
nr3 = []
for i in range(3):
nr3.append(nr[i])
while not check_nr_size(nr3[i], 3):
nr3[i] += 1
s = ' grid = ('
for i in range(3):
s += ' %i' % nr[i]
s += ' ) -- minimal\n'
h.write(s)
s = ' ('
for i in range(3):
s += ' %i' % nr6[i]
s += ' ) -- factors 2, 3, 5, 7, 1*11, 1*13\n'
h.write(s)
s = ' ('
for i in range(3):
s += ' %i' % nr3[i]
s += ' ) -- factors 2, 3, 5\n'
h.write(s)
h.write('\n')
grange = []
s = " Max G-vector indices :"
for idir in range(3):
grange.append((nr[idir] - 1) / 2)
s += " %i" % grange[idir]
h.write(s)
h.write('\n')
if kpt_given:
s = ' k-point = ('
for i in range(3):
s += ' %.9f' % kpt[i]
s += ' )'
h.write(s)
h.write('\n')
ng = 0
g_cryst = []
g_cart = []
e_kin = []
for i in range(-grange[0], grange[0] + 1):
for j in range(-grange[1], grange[1] + 1):
for k in range(-grange[2], grange[2] + 1):
ifl = float(i) + kpt[0]
jfl = float(j) + kpt[1]
kfl = float(k) + kpt[2]
gx = ifl * b[0][0] + jfl * b[1][0] + kfl * b[2][0]
gy = ifl * b[0][1] + jfl * b[1][1] + kfl * b[2][1]
gz = ifl * b[0][2] + jfl * b[1][2] + kfl * b[2][2]
g2 = gx * gx + gy * gy + gz * gz
if bl * bl * g2 < ecut:
ng += 1
g_cryst.append([i, j, k])
gx = float(i) * b[0][0] + float(j) * b[1][0] + float(k) * b[2][0]
gy = float(i) * b[0][1] + float(j) * b[1][1] + float(k) * b[2][1]
gz = float(i) * b[0][2] + float(j) * b[1][2] + float(k) * b[2][2]
g_cart.append([bl * gx, bl * gy, bl * gz])
e_kin.append(bl * bl * g2)
g_sort = []
for i in range(ng):
g_sort.append(i)
if fsort:
e_sort = []
for i in range(ng):
e_sort.append(e_kin[i])
e_sort.sort()
for i in range(ng):
j = e_sort.index(e_kin[i])
e_sort[j] = inf9
g_sort[j] = i
s = ' ng = %i\n' % ng
h.write(s)
h.write('\n')
h.write(' n g1 g2 g3 gx gy gz ekin\n')
h.write(' --------------------------------------------------------------------\n')
for i in range(ng):
s = ' %5i' % (i + 1)
for j in range(3):
s += ' %5i' % g_cryst[g_sort[i]][j]
for j in range(3):
s += ' %9.3f' % g_cart[g_sort[i]][j]
s += ' %15.9f' % e_kin[g_sort[i]]
s += '\n'
h.write(s)
h.write('\n')
h.close()
return 0
def main(argv = None):
if argv is None:
argv = sys.argv
argc = len(argv)
self = "volume.py"
if argv[0][-len(self):] != self:
sys.exit("\n Rename script to %s\n" % self)
if not (argc == 9 or argc == 10):
sys.exit("\n Usage: %s imfn imff ivfn ivff ovfn ovff phas cplx [hole]\n" % self +
" imfn = input matter file name\n" +
" imff = input matter file format\n" +
" (mat|paratec|vasp|espresso|siesta|tbpw|xyz|xsf)\n" +
" ivfn = input volumetric file name\n" +
" ivff = input volumetric file format (a3dr)\n" +
" ovfn = output volumetric file name\n" +
" ovff = output volumetric file format (cube|xsf)\n" +
" phas = remove wavefunction phase (true|false)\n" +
" cplx = complex wavefunction (re|im|abs|abs2)\n" +
" hole = plot hole (true|false)\n")
imfn = argv[1]
imff = argv[2].lower()
ivfn = argv[3]
ivff = argv[4].lower()
ovfn = argv[5]
ovff = argv[6].lower()
if imff == 'mat':
ierr, mat = mat_read(imfn)
elif imff == 'paratec':
ierr, mat = paratec_read(imfn)
elif imff == 'vasp':
ierr, mat = vasp_read(imfn)
elif imff == 'espresso':
ierr, mat = espresso_read(imfn)
elif imff == 'siesta':
ierr, mat = siesta_read(imfn)
elif imff == 'tbpw':
ierr, mat = tbpw_read(imfn)
elif imff == 'xyz':
ierr, mat = xyz_read(imfn)
elif imff == 'xsf':
ierr, mat = xsf_read(imfn)
else:
sys.exit("\n Error: invalid input format %s\n" % imff)
if ierr != 0:
sys.exit("\n Error: unable to read file %s\n" % imfn)
ierr = mat_check(mat)
if ierr != 0:
sys.exit("\n Error: invalid content in file %s\n" % imfn)
if ivff == 'a3dr':
ierr, state, energy, holpos, latvec, grid, psi = a3dr_read(ivfn)
else:
sys.exit("\n Error: invalid input format %s\n" % ivff)
if ierr != 0:
sys.exit("\n Error: unable to read file %s\n" % ivfn)
format = format_index2mat[0]
so = [0.0, 0.0, 0.0]
# temporary hack for a3dr format
# lattice vectors in a3dr file are written in %.6f format
# in paratec benzene example, lattice vectors read from a3dr file
# differ from lattice vectors read from paratec input file
# this results in identical atoms written to rho.cube
# (total of 16 atoms instead of 12 atoms)
# this hack computes the supercell dimensions and
# replaces the lattice vectors read from a3dr file
# with the lattice vectors read from the input file
# multiplied by the supercell dimensions
mat = mat_format(mat, mat['fc'], mat['fo'], format, mat['fp'])
a1 = mat['lv'][0]
a2 = mat['lv'][1]
a3 = mat['lv'][2]
b1 = latvec[0]
b2 = latvec[1]
b3 = latvec[2]
n1 = int(round((a1[0] * b1[0] + a1[1] * b1[1] + a1[2] * b1[2]) / (a1[0]**2 + a1[1]**2 + a1[2]**2)))
n2 = int(round((a2[0] * b2[0] + a2[1] * b2[1] + a2[2] * b2[2]) / (a2[0]**2 + a2[1]**2 + a2[2]**2)))
n3 = int(round((a3[0] * b3[0] + a3[1] * b3[1] + a3[2] * b3[2]) / (a3[0]**2 + a3[1]**2 + a3[2]**2)))
b1 = [n1 * a1[0], n1 * a1[1], n1 * a1[2]]
b2 = [n2 * a2[0], n2 * a2[1], n2 * a2[2]]
b3 = [n3 * a3[0], n3 * a3[1], n3 * a3[2]]
latvec = [b1, b2, b3]
# end of hack
sv = latvec
smin, smax, si, mat = mat_replicate(mat, so, sv, format)
if mat['fo'] != format and mat['fv'] != format and mat['fp'] != format:
sys.exit("\n Error: unable to make supercell\n")
if argc > 9 and holpos != []:
ierr, hole = boolean_input(argv[9])
if ierr != 0:
sys.exit("\n Error: invalid hole %s\n" % argv[9])
if hole != 0:
mat['as'].append(0)
mat['ap'].append(holpos)
mat['na'] += 1
mat['ns'] = len(mat_species(mat['na'], mat['as']))
ierr, phas = boolean_input(argv[7])
if ierr != 0:
sys.exit("\n Error: invalid phase %s\n" % argv[7])
if phas != 0:
rmax = 0.0
for i in range(grid[0]):
for j in range(grid[1]):
for k in range(grid[2]):
r = math.sqrt(math.pow(psi[k][j][i][0], 2) + math.pow(psi[k][j][i][1], 2))
if r > rmax:
rmax = r
phase = math.atan2(psi[k][j][i][1], psi[k][j][i][0])
cs = math.cos(phase)
sn = math.sin(phase)
for i in range(grid[0]):
for j in range(grid[1]):
for k in range(grid[2]):
x = psi[k][j][i][0]
y = psi[k][j][i][1]
psi[k][j][i][0] = cs * x + sn * y
psi[k][j][i][1] = -sn * x + cs * y
ierr, cplx = cplx_input(argv[8])
if ierr != 0:
sys.exit("\n Error: invalid cplx %s\n" % argv[8])
phi = []
for i in range(grid[0]):
phi.append([])
for j in range(grid[1]):
phi[i].append([])
for k in range(grid[2]):
if cplx == 0:
chi = psi[k][j][i][0]
elif cplx == 1:
chi = psi[k][j][i][1]
elif cplx == 2:
chi = math.sqrt(math.pow(psi[k][j][i][0], 2) + math.pow(psi[k][j][i][1], 2))
elif cplx == 3:
chi = math.pow(psi[k][j][i][0], 2) + math.pow(psi[k][j][i][1], 2)
else:
chi = 0.0
if phas != 0 and (cplx == 2 or cplx == 3) and psi[k][j][i][0] < 0.0:
chi = -chi
phi[i][j].append(chi)
if ovff == 'cube':
i = 0
elif ovff == 'xsf':
i = 1
else:
sys.exit("\n Error: invalid output format %s\n" % ovff)
fc = format_index2mat[i]
fo = format_index2mat[i]
fv = format_index2mat[i]
fp = format_index2mat[i]
mat = mat_format(mat, fc, fo, fv, fp)
if mat['fc'] != fc or mat['fo'] != fo or mat['fv'] != fv or mat['fp'] != fp:
sys.exit("\n Error: invalid content in file %s\n" % imfn)
na = mat['na']
aspecies = []
for i in range(na):
aspecies.append(mat['as'][i])
acharge = []
for i in range(na):
acharge.append(float(mat['as'][i]))
aposition = []
for i in range(na):
aposition.append([])
for j in range(3):
aposition[i].append(mat['ap'][i][j])
origin = []
for j in range(3):
origin.append(mat['lo'][j])
latvec = []
for i in range(3):
latvec.append([])
for j in range(3):
latvec[i].append(mat['lv'][i][j])
step = []
for i in range(3):
step.append([])
for j in range(3):
step[i].append(latvec[i][j] / float(grid[i]))
if ovff == 'cube':
ierr = cub_write(ovfn, state, energy, na, aspecies, acharge, aposition, grid, origin, step, phi)
elif ovff == 'xsf':
ierr = xsf_write(ovfn, state, energy, na, aspecies, aposition, grid, origin, latvec, phi)
else:
sys.exit("\n Error: invalid output format %s\n" % ovff)
if ierr != 0:
sys.exit("\n Error: unable to write file %s\n" % ovfn)
return 0