def readPLD(fname, norbitals, natoms):
"""
Read unformatted siesta PLD file
"""
import collections
# use struct library to read mixed data type from binary
import struct
PLD_tuple = collections.namedtuple('PLD', ['max_rcut', 'orb2ao',
'orb2uorb', 'orb2occ',
'atm2sp', 'atm2shift',
'coord_sc', 'cell',
'nunit_cells'])
fh = FortranFile(fname)
orb2ao = np.zeros((norbitals), dtype=int)
orb2uorb = np.zeros((norbitals), dtype=int)
orb2occ = np.zeros((norbitals), dtype=float)
max_rcut = fh.readReals('d')
for iorb in range(norbitals):
dat = fh.readRecord()
dat_size = struct.calcsize('iid')
val_list = struct.unpack('iid', dat[0:dat_size])
orb2ao[iorb] = val_list[0]
orb2uorb[iorb] = val_list[1]
orb2occ[iorb] = val_list[2]
atm2sp = np.zeros((natoms), dtype=int)
atm2shift = np.zeros((natoms + 1), dtype=int)
for iatm in range(natoms):
atm2sp[iatm] = fh.readInts('i')[0]
for iatm in range(natoms + 1):
atm2shift[iatm] = fh.readInts('i')[0]
cell = np.zeros((3, 3), dtype=float)
nunit_cells = np.zeros((3), dtype=int)
for i in range(3):
cell[i, :] = fh.readReals('d')
nunit_cells = fh.readInts('i')
coord_sc = np.zeros((natoms, 3), dtype=float)
for iatm in range(natoms):
coord_sc[iatm, :] = fh.readReals('d')
fh.close()
return PLD_tuple(max_rcut, orb2ao, orb2uorb, orb2occ, atm2sp, atm2shift,
coord_sc, cell, nunit_cells)
def readPLD(fname, norbitals, natoms):
"""
Read unformatted siesta PLD file
"""
import collections
# use struct library to read mixed data type from binary
import struct
PLD_tuple = collections.namedtuple('PLD', [
'max_rcut', 'orb2ao', 'orb2uorb', 'orb2occ', 'atm2sp', 'atm2shift',
'coord_sc', 'cell', 'nunit_cells'
])
fh = FortranFile(fname)
orb2ao = np.zeros((norbitals), dtype=int)
orb2uorb = np.zeros((norbitals), dtype=int)
orb2occ = np.zeros((norbitals), dtype=float)
max_rcut = fh.readReals('d')
for iorb in range(norbitals):
dat = fh.readRecord()
dat_size = struct.calcsize('iid')
val_list = struct.unpack('iid', dat[0:dat_size])
orb2ao[iorb] = val_list[0]
orb2uorb[iorb] = val_list[1]
orb2occ[iorb] = val_list[2]
atm2sp = np.zeros((natoms), dtype=int)
atm2shift = np.zeros((natoms + 1), dtype=int)
for iatm in range(natoms):
atm2sp[iatm] = fh.readInts('i')[0]
for iatm in range(natoms + 1):
atm2shift[iatm] = fh.readInts('i')[0]
cell = np.zeros((3, 3), dtype=float)
nunit_cells = np.zeros((3), dtype=int)
for i in range(3):
cell[i, :] = fh.readReals('d')
nunit_cells = fh.readInts('i')
coord_sc = np.zeros((natoms, 3), dtype=float)
for iatm in range(natoms):
coord_sc[iatm, :] = fh.readReals('d')
fh.close()
return PLD_tuple(max_rcut, orb2ao, orb2uorb, orb2occ, atm2sp, atm2shift,
coord_sc, cell, nunit_cells)
def read_rho(fname):
"Read unformatted Siesta charge density file"
# TODO:
#
# Handle formatted and NetCDF files.
#
# Siesta source code (at least 2.0.2) can possibly also
# save RHO as a _formatted_ file (the source code seems
# prepared, but there seems to be no fdf-options for it though).
# Siesta >= 3 has support for saving RHO as a NetCDF file
# (according to manual)
fh = FortranFile(fname)
# Read (but ignore) unit cell vectors
x = fh.readReals('d')
if len(x) != 3 * 3:
raise IOError('Failed to read cell vectors')
# Read number of grid points and spin components
x = fh.readInts()
if len(x) != 4:
raise IOError('Failed to read grid size')
gpts = x # number of 'X', 'Y', 'Z', 'spin' gridpoints
rho = np.zeros(gpts)
for ispin in range(gpts[3]):
for n3 in range(gpts[2]):
for n2 in range(gpts[1]):
x = fh.readReals('f')
if len(x) != gpts[0]:
raise IOError('Failed to read RHO[:,%i,%i,%i]' %
(n2, n3, ispin))
rho[:, n2, n3, ispin] = x
fh.close()
return rho
def read_rho(fname):
"Read unformatted Siesta charge density file"
# TODO:
#
# Handle formatted and NetCDF files.
#
# Siesta source code (at least 2.0.2) can possibly also
# save RHO as a _formatted_ file (the source code seems
# prepared, but there seems to be no fdf-options for it though).
# Siesta >= 3 has support for saving RHO as a NetCDF file
# (according to manual)
fh = FortranFile(fname)
# Read (but ignore) unit cell vectors
x = fh.readReals('d')
if len(x) != 3 * 3:
raise IOError('Failed to read cell vectors')
# Read number of grid points and spin components
x = fh.readInts()
if len(x) != 4:
raise IOError('Failed to read grid size')
gpts = x # number of 'X', 'Y', 'Z', 'spin' gridpoints
rho = np.zeros(gpts)
for ispin in range(gpts[3]):
for n3 in range(gpts[2]):
for n2 in range(gpts[1]):
x = fh.readReals('f')
if len(x) != gpts[0]:
raise IOError('Failed to read RHO[:,%i,%i,%i]' %
(n2, n3, ispin))
rho[:, n2, n3, ispin] = x
fh.close()
return rho
def readDIM(fname):
"""
Read unformatted siesta DIM file
"""
import collections
DIM_tuple = collections.namedtuple('DIM', [
'natoms_sc', 'norbitals_sc', 'norbitals', 'nspin', 'nnonzero',
'natoms_interacting'
])
fh = FortranFile(fname)
natoms_sc = fh.readInts('i')[0]
norbitals_sc = fh.readInts('i')[0]
norbitals = fh.readInts('i')[0]
nspin = fh.readInts('i')[0]
nnonzero = fh.readInts('i')[0]
natoms_interacting = fh.readInts('i')[0]
fh.close()
return DIM_tuple(natoms_sc, norbitals_sc, norbitals, nspin, nnonzero,
natoms_interacting)
def readDIM(fname):
"""
Read unformatted siesta DIM file
"""
import collections
DIM_tuple = collections.namedtuple('DIM', ['natoms_sc', 'norbitals_sc',
'norbitals', 'nspin',
'nnonzero',
'natoms_interacting'])
fh = FortranFile(fname)
natoms_sc = fh.readInts('i')[0]
norbitals_sc = fh.readInts('i')[0]
norbitals = fh.readInts('i')[0]
nspin = fh.readInts('i')[0]
nnonzero = fh.readInts('i')[0]
natoms_interacting = fh.readInts('i')[0]
fh.close()
return DIM_tuple(natoms_sc, norbitals_sc, norbitals, nspin,
nnonzero, natoms_interacting)
def readHSX(fname):
"""
Read unformatted siesta HSX file
"""
import collections
HSX_tuple = collections.namedtuple('HSX', [
'norbitals', 'norbitals_sc', 'nspin', 'nonzero', 'is_gamma',
'sc_orb2uc_orb', 'row2nnzero', 'sparse_ind2column', 'H_sparse',
'S_sparse', 'aB2RaB_sparse', 'total_elec_charge', 'temp'
])
fh = FortranFile(fname)
norbitals, norbitals_sc, nspin, nonzero = fh.readInts('i')
is_gamma = fh.readInts('i')[0]
sc_orb2uc_orb = 0
if is_gamma == 0:
sc_orb2uc_orb = fh.readInts('i')
row2nnzero = fh.readInts('i')
sum_row2nnzero = np.sum(row2nnzero)
if (sum_row2nnzero != nonzero):
raise ValueError('sum_row2nnzero != nonzero: {0} != {1}'.format(
sum_row2nnzero, nonzero))
row2displ = np.zeros((norbitals), dtype=int)
for i in range(1, norbitals):
row2displ[i] = row2displ[i - 1] + row2nnzero[i - 1]
max_nonzero = np.max(row2nnzero)
int_buff = np.zeros((max_nonzero), dtype=int)
sparse_ind2column = np.zeros((nonzero))
# Fill the rows for each index in *_sparse arrays
for irow in range(norbitals):
f = row2nnzero[irow]
int_buff[0:f] = fh.readInts('i')
# read set of rows where nonzero elements reside
d = row2displ[irow]
sparse_ind2column[d:d + f] = int_buff[0:f]
# END of Fill the rows for each index in *_sparse arrays
# allocate H, S and X matrices
sp_buff = np.zeros((max_nonzero), dtype=float)
H_sparse = np.zeros((nonzero, nspin), dtype=float)
S_sparse = np.zeros((nonzero), dtype=float)
aB2RaB_sparse = np.zeros((3, nonzero), dtype=float)
# Read the data to H_sparse array
for ispin in range(nspin):
for irow in range(norbitals):
d = row2displ[irow]
f = row2nnzero[irow]
sp_buff[0:f] = fh.readReals('f')
H_sparse[d:d + f, ispin] = sp_buff[0:f]
# Read the data to S_sparse array
for irow in range(norbitals):
f = row2nnzero[irow]
d = row2displ[irow]
sp_buff[0:f] = fh.readReals('f')
S_sparse[d:d + f] = sp_buff[0:f]
total_elec_charge, temp = fh.readReals('d')
sp_buff = np.zeros((3 * max_nonzero), dtype=float)
# Read the data to S_sparse array
for irow in range(norbitals):
f = row2nnzero[irow]
d = row2displ[irow]
sp_buff[0:3 * f] = fh.readReals('f')
aB2RaB_sparse[0, d:d + f] = sp_buff[0:f]
aB2RaB_sparse[1, d:d + f] = sp_buff[f:2 * f]
aB2RaB_sparse[2, d:d + f] = sp_buff[2 * f:3 * f]
fh.close()
return HSX_tuple(norbitals, norbitals_sc, nspin, nonzero, is_gamma,
sc_orb2uc_orb, row2nnzero, sparse_ind2column, H_sparse,
S_sparse, aB2RaB_sparse, total_elec_charge, temp)
def readWFSX(fname):
"""
Read unformatted siesta WFSX file
"""
import collections
# use struct library to read mixed data type from binary
import struct
WFSX_tuple = collections.namedtuple('WFSX', [
'nkpoints', 'nspin', 'norbitals', 'gamma', 'orb2atm', 'orb2strspecies',
'orb2ao', 'orb2n', 'orb2strsym', 'kpoints', 'DFT_E', 'DFT_X',
'mo_spin_kpoint_2_is_read'
])
fh = FortranFile(fname)
nkpoints, gamma = fh.readInts('i')
nspin = fh.readInts('i')[0]
norbitals = fh.readInts('i')[0]
orb2atm = np.zeros((norbitals), dtype=int)
orb2strspecies = []
orb2ao = np.zeros((norbitals), dtype=int)
orb2n = np.zeros((norbitals), dtype=int)
orb2strsym = []
# for string list are better to select all the string length
dat_size = struct.calcsize('i20sii20s')
dat = fh.readRecord()
ind_st = 0
ind_fn = dat_size
for iorb in range(norbitals):
val_list = struct.unpack('i20sii20s', dat[ind_st:ind_fn])
orb2atm[iorb] = val_list[0]
orb2strspecies.append(val_list[1])
orb2ao[iorb] = val_list[2]
orb2n[iorb] = val_list[3]
orb2strsym.append(val_list[4])
ind_st = ind_st + dat_size
ind_fn = ind_fn + dat_size
orb2strspecies = np.array(orb2strspecies)
orb2strsym = np.array(orb2strsym)
kpoints = np.zeros((3, nkpoints), dtype=np.float64)
DFT_E = np.zeros((norbitals, nspin, nkpoints), dtype=np.float64)
if (gamma == 1):
DFT_X = np.zeros((1, norbitals, norbitals, nspin, nkpoints),
dtype=np.float64)
eigenvector = np.zeros((1, norbitals), dtype=float)
else:
DFT_X = np.zeros((2, norbitals, norbitals, nspin, nkpoints),
dtype=np.float64)
eigenvector = np.zeros((2, norbitals), dtype=float)
mo_spin_kpoint_2_is_read = np.zeros((norbitals, nspin, nkpoints),
dtype=bool)
mo_spin_kpoint_2_is_read[0:norbitals, 0:nspin, 0:nkpoints] = False
dat_size = struct.calcsize('iddd')
for ikpoint in range(nkpoints):
for ispin in range(nspin):
dat = fh.readRecord()
val_list = struct.unpack('iddd', dat[0:dat_size])
ikpoint_in = val_list[0] - 1
kpoints[0:3, ikpoint] = val_list[1:4]
if (ikpoint != ikpoint_in):
raise ValueError('siesta_get_wfsx: ikpoint != ikpoint_in')
ispin_in = fh.readInts('i')[0] - 1
if (ispin_in > nspin - 1):
msg = 'siesta_get_wfsx: err: ispin_in>nspin\n \
siesta_get_wfsx: ikpoint, ispin, ispin_in = \
{0} {1} {2}\n siesta_get_wfsx'.format(
ikpoint, ispin, ispin_in)
raise ValueError(msg)
norbitals_in = fh.readInts('i')[0]
if (norbitals_in > norbitals):
msg = 'siesta_get_wfsx: err: norbitals_in>norbitals\n \
siesta_get_wfsx: ikpoint, norbitals, norbitals_in = \
{0} {1} {2}\n siesta_get_wfsx'.format(
ikpoint, norbitals, norbitals_in)
raise ValueError(msg)
for imolecular_orb in range(norbitals_in):
imolecular_orb_in = fh.readInts('i')[0] - 1
if (imolecular_orb_in > norbitals - 1):
msg = """
siesta_get_wfsx: err: imolecular_orb_in>norbitals\n
siesta_get_wfsx: ikpoint, norbitals,
imolecular_orb_in = {0} {1} {2}\n
siesta_get_wfsx""".format(ikpoint, norbitals,
imolecular_orb_in)
raise ValueError(msg)
real_E_eV = fh.readReals('d')[0]
eigenvector = fh.readReals('f')
DFT_E[imolecular_orb_in, ispin_in,
ikpoint] = real_E_eV / 13.60580
DFT_X[:, :, imolecular_orb_in, ispin_in, ikpoint] = eigenvector
mo_spin_kpoint_2_is_read[imolecular_orb_in, ispin_in,
ikpoint] = True
if (not all(mo_spin_kpoint_2_is_read[:, ispin_in, ikpoint])):
msg = 'siesta_get_wfsx: warn: .not. all(mo_spin_k_2_is_read)'
print('mo_spin_kpoint_2_is_read = ', mo_spin_kpoint_2_is_read)
raise ValueError(msg)
fh.close()
return WFSX_tuple(nkpoints, nspin, norbitals, gamma, orb2atm,
orb2strspecies, orb2ao, orb2n, orb2strsym, kpoints,
DFT_E, DFT_X, mo_spin_kpoint_2_is_read)
def readWFSX(fname):
"""
Read unformatted siesta WFSX file
"""
import collections
# use struct library to read mixed data type from binary
import struct
WFSX_tuple = collections.namedtuple('WFSX',
['nkpoints', 'nspin', 'norbitals',
'gamma', 'orb2atm', 'orb2strspecie',
'orb2ao', 'orb2n', 'orb2strsym',
'kpoints', 'DFT_E', 'DFT_X',
'mo_spin_kpoint_2_is_read'])
fh = FortranFile(fname)
nkpoints, gamma = fh.readInts('i')
nspin = fh.readInts('i')[0]
norbitals = fh.readInts('i')[0]
orb2atm = np.zeros((norbitals), dtype=int)
orb2strspecie = []
orb2ao = np.zeros((norbitals), dtype=int)
orb2n = np.zeros((norbitals), dtype=int)
orb2strsym = []
# for string list are better to select all the string length
dat_size = struct.calcsize('i20sii20s')
dat = fh.readRecord()
ind_st = 0
ind_fn = dat_size
for iorb in range(norbitals):
val_list = struct.unpack('i20sii20s', dat[ind_st:ind_fn])
orb2atm[iorb] = val_list[0]
orb2strspecie.append(val_list[1])
orb2ao[iorb] = val_list[2]
orb2n[iorb] = val_list[3]
orb2strsym.append(val_list[4])
ind_st = ind_st + dat_size
ind_fn = ind_fn + dat_size
orb2strspecie = np.array(orb2strspecie)
orb2strsym = np.array(orb2strsym)
kpoints = np.zeros((3, nkpoints), dtype=np.float64)
DFT_E = np.zeros((norbitals, nspin, nkpoints), dtype=np.float64)
if (gamma == 1):
DFT_X = np.zeros((1, norbitals, norbitals, nspin, nkpoints),
dtype=np.float64)
eigenvector = np.zeros((1, norbitals), dtype=float)
else:
DFT_X = np.zeros((2, norbitals, norbitals, nspin, nkpoints),
dtype=np.float64)
eigenvector = np.zeros((2, norbitals), dtype=float)
mo_spin_kpoint_2_is_read = np.zeros((norbitals, nspin, nkpoints),
dtype=bool)
mo_spin_kpoint_2_is_read[0:norbitals, 0:nspin, 0:nkpoints] = False
dat_size = struct.calcsize('iddd')
for ikpoint in range(nkpoints):
for ispin in range(nspin):
dat = fh.readRecord()
val_list = struct.unpack('iddd', dat[0:dat_size])
ikpoint_in = val_list[0] - 1
kpoints[0:3, ikpoint] = val_list[1:4]
if (ikpoint != ikpoint_in):
raise ValueError('siesta_get_wfsx: ikpoint != ikpoint_in')
ispin_in = fh.readInts('i')[0] - 1
if (ispin_in > nspin - 1):
msg = 'siesta_get_wfsx: err: ispin_in>nspin\n \
siesta_get_wfsx: ikpoint, ispin, ispin_in = \
{0} {1} {2}\n siesta_get_wfsx'.format(ikpoint,
ispin, ispin_in)
raise ValueError(msg)
norbitals_in = fh.readInts('i')[0]
if (norbitals_in > norbitals):
msg = 'siesta_get_wfsx: err: norbitals_in>norbitals\n \
siesta_get_wfsx: ikpoint, norbitals, norbitals_in = \
{0} {1} {2}\n siesta_get_wfsx'.format(ikpoint,
norbitals,
norbitals_in)
raise ValueError(msg)
for imolecular_orb in range(norbitals_in):
imolecular_orb_in = fh.readInts('i')[0] - 1
if (imolecular_orb_in > norbitals - 1):
msg = """
siesta_get_wfsx: err: imolecular_orb_in>norbitals\n
siesta_get_wfsx: ikpoint, norbitals,
imolecular_orb_in = {0} {1} {2}\n
siesta_get_wfsx""".format(ikpoint, norbitals,
imolecular_orb_in)
raise ValueError(msg)
real_E_eV = fh.readReals('d')[0]
eigenvector = fh.readReals('f')
DFT_E[imolecular_orb_in, ispin_in,
ikpoint] = real_E_eV / 13.60580
DFT_X[:, :, imolecular_orb_in, ispin_in,
ikpoint] = eigenvector
mo_spin_kpoint_2_is_read[imolecular_orb_in, ispin_in,
ikpoint] = True
if (not all(mo_spin_kpoint_2_is_read[:, ispin_in, ikpoint])):
msg = 'siesta_get_wfsx: warn: .not. all(mo_spin_k_2_is_read)'
print('mo_spin_kpoint_2_is_read = ', mo_spin_kpoint_2_is_read)
raise ValueError(msg)
fh.close()
return WFSX_tuple(nkpoints, nspin, norbitals, gamma, orb2atm,
orb2strspecie, orb2ao, orb2n, orb2strsym,
kpoints, DFT_E, DFT_X, mo_spin_kpoint_2_is_read)
def readHSX(fname):
"""
Read unformatted siesta HSX file
"""
import collections
HSX_tuple = collections.namedtuple('HSX',
['norbitals', 'norbitals_sc', 'nspin',
'nonzero', 'is_gamma', 'sc_orb2uc_orb',
'row2nnzero', 'sparse_ind2column',
'H_sparse', 'S_sparse',
'aB2RaB_sparse', 'total_elec_charge',
'temp'])
fh = FortranFile(fname)
norbitals, norbitals_sc, nspin, nonzero = fh.readInts('i')
is_gamma = fh.readInts('i')[0]
sc_orb2uc_orb = 0
if is_gamma == 0:
sc_orb2uc_orb = fh.readInts('i')
row2nnzero = fh.readInts('i')
sum_row2nnzero = np.sum(row2nnzero)
if (sum_row2nnzero != nonzero):
raise ValueError('sum_row2nnzero != nonzero: {0} != {1}'
.format(sum_row2nnzero, nonzero))
row2displ = np.zeros((norbitals), dtype=int)
for i in range(1, norbitals):
row2displ[i] = row2displ[i - 1] + row2nnzero[i - 1]
max_nonzero = np.max(row2nnzero)
int_buff = np.zeros((max_nonzero), dtype=int)
sparse_ind2column = np.zeros((nonzero))
# Fill the rows for each index in *_sparse arrays
for irow in range(norbitals):
f = row2nnzero[irow]
int_buff[0:f] = fh.readInts('i')
# read set of rows where nonzero elements reside
d = row2displ[irow]
sparse_ind2column[d:d + f] = int_buff[0:f]
# END of Fill the rows for each index in *_sparse arrays
# allocate H, S and X matrices
sp_buff = np.zeros((max_nonzero), dtype=float)
H_sparse = np.zeros((nonzero, nspin), dtype=float)
S_sparse = np.zeros((nonzero), dtype=float)
aB2RaB_sparse = np.zeros((3, nonzero), dtype=float)
# Read the data to H_sparse array
for ispin in range(nspin):
for irow in range(norbitals):
d = row2displ[irow]
f = row2nnzero[irow]
sp_buff[0:f] = fh.readReals('f')
H_sparse[d:d + f, ispin] = sp_buff[0:f]
# Read the data to S_sparse array
for irow in range(norbitals):
f = row2nnzero[irow]
d = row2displ[irow]
sp_buff[0:f] = fh.readReals('f')
S_sparse[d:d + f] = sp_buff[0:f]
total_elec_charge, temp = fh.readReals('d')
sp_buff = np.zeros((3 * max_nonzero), dtype=float)
# Read the data to S_sparse array
for irow in range(norbitals):
f = row2nnzero[irow]
d = row2displ[irow]
sp_buff[0: 3 * f] = fh.readReals('f')
aB2RaB_sparse[0, d:d + f] = sp_buff[0:f]
aB2RaB_sparse[1, d:d + f] = sp_buff[f:2 * f]
aB2RaB_sparse[2, d:d + f] = sp_buff[2 * f:3 * f]
fh.close()
return HSX_tuple(norbitals, norbitals_sc, nspin, nonzero, is_gamma,
sc_orb2uc_orb, row2nnzero, sparse_ind2column, H_sparse,
S_sparse, aB2RaB_sparse, total_elec_charge, temp)