mirror of
https://github.com/triqs/dft_tools
synced 2024-06-26 15:12:18 +02:00
Added a preliminary version of VaspConverter
This preliminary version is untested and might not even run. Here, almost all relevant input (apart from symmetries and miscellaneous) is implemented and conventions adpoted in DftTools are accomodated.
This commit is contained in:
Oleg E. Peil
Michel Ferrero
parent
d70dca3dd7
commit
84061edc4b
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@ -26,6 +26,7 @@ from pytriqs.archive import *
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from converter_tools import *
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import os.path
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import simplejson as json
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#from plotools import ProjectorGroup, ProjectorShell
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class VaspConverter(ConverterTools):
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"""
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@ -93,152 +94,280 @@ class VaspConverter(ConverterTools):
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"""
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Reads the input files, and stores the data in the HDFfile
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"""
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energy_unit = 1.0 # VASP interface always uses eV
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k_dep_projection = 1
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symm_op = 1 # Use symmetry groups for the k-sum
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# Read and write only on the master node
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if not (mpi.is_master_node()): return
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mpi.report("Reading input from %s..."%self.dft_file)
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# R is a generator : each R.Next() will return the next number in the file
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jheader, rf = self.read_header_and_data(self, self.ctrl_file)
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jheader, rf = self.read_header_and_data(self.ctrl_file)
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ctrl_head = json.loads(jheader)
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ng = ctrl_head['ngroups']
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nk = ctrl_head['nk']
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ns = ctrl_head['ns']
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nc_flag = ctrl_head['nc_flag']
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n_k = ctrl_head['nk']
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# Note the difference in name conventions!
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SP = ctrl_head['ns']
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SO = ctrl_head['nc_flag']
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kpts = numpy.zeros((nk, 3))
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kweights = numpy.zeros(nk)
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bz_weights = numpy.zeros(nk)
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try:
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for ik in xrange(nk):
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kx, ky, kz = rf.next(), rf.next(), rf.next()
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kpts[ik, :] = kx, ky, kz
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kweights[ik] = rf.next()
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bz_weights[ik] = rf.next()
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except StopIteration:
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raise "VaspConverter: error reading %s"%self.ctrl_file
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# if nc_flag:
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## TODO: check this
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# n_spin_blocs = 1
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# else:
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# n_spin_blocs = ns
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n_spin_blocs = SP + 1 - SO
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# Read PLO groups
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for ig in xrange(ng):
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# First, we read everything into a temporary data structure
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# TODO: think about multiple shell groups and how to map them on h5 structures
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assert ng == 1, "Only one group is allowed at the moment"
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try:
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energy_unit = R.next() # read the energy convertion factor
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n_k = int(R.next()) # read the number of k points
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k_dep_projection = 1
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SP = int(R.next()) # flag for spin-polarised calculation
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SO = int(R.next()) # flag for spin-orbit calculation
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charge_below = R.next() # total charge below energy window
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density_required = R.next() # total density required, for setting the chemical potential
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symm_op = 1 # Use symmetry groups for the k-sum
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for ig in xrange(ng):
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gr_file = self.basename + '.pg%i'%(ig + 1)
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jheader, rf = self.read_header_and_data(gr_file)
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gr_head = json.loads(jheader)
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# the information on the non-correlated shells is not important here, maybe skip:
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n_shells = int(R.next()) # number of shells (e.g. Fe d, As p, O p) in the unit cell,
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# corresponds to index R in formulas
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# now read the information about the shells (atom, sort, l, dim):
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shell_entries = ['atom', 'sort', 'l', 'dim']
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shells = [ {name: int(val) for name, val in zip(shell_entries, R)} for ish in range(n_shells) ]
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e_win = gr_head['ewindow']
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nb_max = gr_head['nb_max']
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p_shells = gr_head['shells']
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density_required = gr_head['nelect']
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charge_below = 0.0 # This is not defined in VASP interface
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n_corr_shells = int(R.next()) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
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# corresponds to index R in formulas
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# now read the information about the shells (atom, sort, l, dim, SO flag, irep):
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corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
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corr_shells = [ {name: int(val) for name, val in zip(corr_shell_entries, R)} for icrsh in range(n_corr_shells) ]
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# TODO: generalize this to the case of multiple shell groups
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n_shells = 0 # No non-correlated shells at the moment
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# determine the number of inequivalent correlated shells and maps, needed for further reading
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n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self,corr_shells)
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# Note that in the DftTools convention each site gives a separate correlated shell!
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n_corr_shells = sum([len(sh['ion_list']) for sh in p_shells])
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corr_shells = []
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shion_to_corr_shell = [[] for ish in xrange(len(p_shells))]
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icsh = 0
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for ish, sh in enumerate(p_shells):
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ion_list = sh['ion_list']
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for i, ion in enumerate(ion_list):
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pars = {}
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pars['atom'] = ion
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pars['sort'] = sh['ion_sort']
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pars['l'] = sh['lorb']
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pars['dim'] = sh['ndim']
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pars['SO'] = SO
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# TODO: check what 'irep' entry does (it seems to be very specific to dmftproj)
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pars['irep'] = 0
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corr_shells.append(pars)
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shion_to_corr_shell[ish].append(i)
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# FIXME: atomic sorts in Wien2K are not the same as in VASP.
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# A symmetry analysis from OUTCAR or symmetry file should be used
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# to define equivalence classes of sites.
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n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self, corr_shells)
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# NB!: these rotation matrices are specific to Wien2K! Set to identity in VASP
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use_rotations = 1
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rot_mat = [numpy.identity(corr_shells[icrsh]['dim'],numpy.complex_) for icrsh in range(n_corr_shells)]
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# read the matrices
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rot_mat_time_inv = [0 for i in range(n_corr_shells)]
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for icrsh in range(n_corr_shells):
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for i in range(corr_shells[icrsh]['dim']): # read real part:
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for j in range(corr_shells[icrsh]['dim']):
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rot_mat[icrsh][i,j] = R.next()
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for i in range(corr_shells[icrsh]['dim']): # read imaginary part:
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for j in range(corr_shells[icrsh]['dim']):
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rot_mat[icrsh][i,j] += 1j * R.next()
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if (SP==1): # read time inversion flag:
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rot_mat_time_inv[icrsh] = int(R.next())
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# Read here the info for the transformation of the basis:
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# TODO: implement transformation matrices
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n_reps = [1 for i in range(n_inequiv_shells)]
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dim_reps = [0 for i in range(n_inequiv_shells)]
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T = []
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for ish in range(n_inequiv_shells):
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n_reps[ish] = int(R.next()) # number of representatives ("subsets"), e.g. t2g and eg
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dim_reps[ish] = [int(R.next()) for i in range(n_reps[ish])] # dimensions of the subsets
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n_reps[ish] = 1 # Always 1 in VASP
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ineq_first = inequiv_to_corr[ish]
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dim_reps[ish] = [corr_shell[ineq_first]['dim']] # Just the dimension of the shell
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# The transformation matrix:
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# is of dimension 2l+1 without SO, and 2*(2l+1) with SO!
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ll = 2*corr_shells[inequiv_to_corr[ish]]['l']+1
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ll = 2 * corr_shells[inequiv_to_corr[ish]]['l']+1
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lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
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T.append(numpy.zeros([lmax,lmax],numpy.complex_))
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# TODO: at the moment put T-matrices to identities
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T.append(numpy.identity(lmax, numpy.complex_))
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# now read it from file:
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for i in range(lmax):
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for j in range(lmax):
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T[ish][i,j] = R.next()
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for i in range(lmax):
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for j in range(lmax):
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T[ish][i,j] += 1j * R.next()
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# Spin blocks to be read:
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n_spin_blocs = SP + 1 - SO
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# read the list of n_orbitals for all k points
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n_orbitals = numpy.zeros([n_k,n_spin_blocs],numpy.int)
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for isp in range(n_spin_blocs):
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for ik in range(n_k):
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n_orbitals[ik,isp] = int(R.next())
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# Initialise the projectors:
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proj_mat = numpy.zeros([n_k,n_spin_blocs,n_corr_shells,max([crsh['dim'] for crsh in corr_shells]),max(n_orbitals)],numpy.complex_)
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# if nc_flag:
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## TODO: implement the noncollinear part
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# raise NotImplementedError("Noncollinear calculations are not implemented")
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# else:
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hopping = numpy.zeros([n_k, n_spin_blocs, nb_max, nb_max], numpy.complex_)
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band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in xrange(n_spin_blocs)]
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n_orbitals = numpy.zeros([n_k, n_spin_blocs], numpy.int)
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# Read the projectors from the file:
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for ik in range(n_k):
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for icrsh in range(n_corr_shells):
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n_orb = corr_shells[icrsh]['dim']
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# first Real part for BOTH spins, due to conventions in dmftproj:
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for isp in range(n_spin_blocs):
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for i in range(n_orb):
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for j in range(n_orbitals[ik][isp]):
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proj_mat[ik,isp,icrsh,i,j] = R.next()
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# now Imag part:
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for isp in range(n_spin_blocs):
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for i in range(n_orb):
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for j in range(n_orbitals[ik][isp]):
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proj_mat[ik,isp,icrsh,i,j] += 1j * R.next()
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# now define the arrays for weights and hopping ...
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bz_weights = numpy.ones([n_k],numpy.float_)/ float(n_k) # w(k_index), default normalisation
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hopping = numpy.zeros([n_k,n_spin_blocs,max(n_orbitals),max(n_orbitals)],numpy.complex_)
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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ib1, ib2 = int(rf.next()), int(rf.next())
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band_window[isp][ik, :2] = ib1, ib2
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nb = ib2 - ib1 + 1
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n_orbitals[ik, isp] = nb
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for ib in xrange(nb):
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hopping[ik, isp, ib, ib] = rf.next()
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# weights in the file
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for ik in range(n_k) : bz_weights[ik] = R.next()
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# if the sum over spins is in the weights, take it out again!!
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sm = sum(bz_weights)
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bz_weights[:] /= sm
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# Projectors
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proj_mat = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, max([crsh['dim'] for crsh in corr_shells]), max(n_orbitals)], numpy.complex_)
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# TODO: implement reading from more than one projector group
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# In 'dmftproj' each ion represents a separate correlated shell.
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# In my interface a 'projected shell' includes sets of ions.
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# How to reconcile this? Two options:
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#
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# 1. Redefine 'projected shell' in my interface to make it correspond to one site only.
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# In this case the list of ions must be defined at the level of the projector group.
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#
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# 2. Split my 'projected shell' to several 'correlated shells' here in the converter.
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#
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# At the moment I choose i.2 for its simplicity. But one should consider possible
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# use cases and decide which solution is to be made permanent.
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#
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for ish, sh in enumerate(p_shells):
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for isp in xrange(n_spin_blocs):
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for ik in xrange(n_k):
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for ion in xrange(len(sh['ion_list'])):
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icsh = shion_to_corr_shell[ish][ion]
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for ilm in xrange(sh['dim']):
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for ib in xrange(n_orbitals[ik, isp]):
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# This is to avoid confusion with the order of arguments
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pr = rf.next()
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pi = rf.next()
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proj_mat[ik, isp, icsh, ilm, ib] = complex(pr, pi)
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# Grab the H
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# we use now the convention of a DIAGONAL Hamiltonian -- convention for Wien2K.
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for isp in range(n_spin_blocs):
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for ik in range(n_k) :
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n_orb = n_orbitals[ik,isp]
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for i in range(n_orb):
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hopping[ik,isp,i,i] = R.next() * energy_unit
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# keep some things that we need for reading parproj:
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things_to_set = ['n_shells','shells','n_corr_shells','corr_shells','n_spin_blocs','n_orbitals','n_k','SO','SP','energy_unit']
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for it in things_to_set: setattr(self,it,locals()[it])
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except StopIteration : # a more explicit error if the file is corrupted.
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raise "Wien2k_converter : reading file %s failed!"%filename
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R.close()
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# Reading done!
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except StopIteration:
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raise "VaspConverter: error reading %s"%self.gr_file
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rf.close()
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#
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# try:
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# energy_unit = R.next() # read the energy convertion factor
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# n_k = int(R.next()) # read the number of k points
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# k_dep_projection = 1
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# SP = int(R.next()) # flag for spin-polarised calculation
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# SO = int(R.next()) # flag for spin-orbit calculation
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# charge_below = R.next() # total charge below energy window
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# density_required = R.next() # total density required, for setting the chemical potential
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# symm_op = 1 # Use symmetry groups for the k-sum
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#
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# # the information on the non-correlated shells is not important here, maybe skip:
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# n_shells = int(R.next()) # number of shells (e.g. Fe d, As p, O p) in the unit cell,
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# # corresponds to index R in formulas
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# # now read the information about the shells (atom, sort, l, dim):
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# shell_entries = ['atom', 'sort', 'l', 'dim']
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# shells = [ {name: int(val) for name, val in zip(shell_entries, R)} for ish in range(n_shells) ]
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#
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# n_corr_shells = int(R.next()) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
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# # corresponds to index R in formulas
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# # now read the information about the shells (atom, sort, l, dim, SO flag, irep):
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# corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
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# corr_shells = [ {name: int(val) for name, val in zip(corr_shell_entries, R)} for icrsh in range(n_corr_shells) ]
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#
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# # determine the number of inequivalent correlated shells and maps, needed for further reading
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# n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self,corr_shells)
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#
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# use_rotations = 1
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# rot_mat = [numpy.identity(corr_shells[icrsh]['dim'],numpy.complex_) for icrsh in range(n_corr_shells)]
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#
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# # read the matrices
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# rot_mat_time_inv = [0 for i in range(n_corr_shells)]
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#
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# for icrsh in range(n_corr_shells):
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# for i in range(corr_shells[icrsh]['dim']): # read real part:
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# for j in range(corr_shells[icrsh]['dim']):
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# rot_mat[icrsh][i,j] = R.next()
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# for i in range(corr_shells[icrsh]['dim']): # read imaginary part:
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# for j in range(corr_shells[icrsh]['dim']):
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# rot_mat[icrsh][i,j] += 1j * R.next()
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#
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# if (SP==1): # read time inversion flag:
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# rot_mat_time_inv[icrsh] = int(R.next())
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#
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# # Read here the info for the transformation of the basis:
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# n_reps = [1 for i in range(n_inequiv_shells)]
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# dim_reps = [0 for i in range(n_inequiv_shells)]
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# T = []
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# for ish in range(n_inequiv_shells):
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# n_reps[ish] = int(R.next()) # number of representatives ("subsets"), e.g. t2g and eg
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# dim_reps[ish] = [int(R.next()) for i in range(n_reps[ish])] # dimensions of the subsets
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#
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# # The transformation matrix:
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# # is of dimension 2l+1 without SO, and 2*(2l+1) with SO!
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# ll = 2*corr_shells[inequiv_to_corr[ish]]['l']+1
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# lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
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# T.append(numpy.zeros([lmax,lmax],numpy.complex_))
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#
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# # now read it from file:
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# for i in range(lmax):
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# for j in range(lmax):
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# T[ish][i,j] = R.next()
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# for i in range(lmax):
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# for j in range(lmax):
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# T[ish][i,j] += 1j * R.next()
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#
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# # Spin blocks to be read:
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# n_spin_blocs = SP + 1 - SO
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#
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# # read the list of n_orbitals for all k points
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# n_orbitals = numpy.zeros([n_k,n_spin_blocs],numpy.int)
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# for isp in range(n_spin_blocs):
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# for ik in range(n_k):
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# n_orbitals[ik,isp] = int(R.next())
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#
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# # Initialise the projectors:
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# proj_mat = numpy.zeros([n_k,n_spin_blocs,n_corr_shells,max([crsh['dim'] for crsh in corr_shells]),max(n_orbitals)],numpy.complex_)
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#
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# # Read the projectors from the file:
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# for ik in range(n_k):
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# for icrsh in range(n_corr_shells):
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# n_orb = corr_shells[icrsh]['dim']
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# # first Real part for BOTH spins, due to conventions in dmftproj:
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# for isp in range(n_spin_blocs):
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# for i in range(n_orb):
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# for j in range(n_orbitals[ik][isp]):
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# proj_mat[ik,isp,icrsh,i,j] = R.next()
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# # now Imag part:
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# for isp in range(n_spin_blocs):
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# for i in range(n_orb):
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# for j in range(n_orbitals[ik][isp]):
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# proj_mat[ik,isp,icrsh,i,j] += 1j * R.next()
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#
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# # now define the arrays for weights and hopping ...
|
||||
# bz_weights = numpy.ones([n_k],numpy.float_)/ float(n_k) # w(k_index), default normalisation
|
||||
# hopping = numpy.zeros([n_k,n_spin_blocs,max(n_orbitals),max(n_orbitals)],numpy.complex_)
|
||||
#
|
||||
# # weights in the file
|
||||
# for ik in range(n_k) : bz_weights[ik] = R.next()
|
||||
#
|
||||
# # if the sum over spins is in the weights, take it out again!!
|
||||
# sm = sum(bz_weights)
|
||||
# bz_weights[:] /= sm
|
||||
#
|
||||
# # Grab the H
|
||||
# # we use now the convention of a DIAGONAL Hamiltonian -- convention for Wien2K.
|
||||
# for isp in range(n_spin_blocs):
|
||||
# for ik in range(n_k) :
|
||||
# n_orb = n_orbitals[ik,isp]
|
||||
# for i in range(n_orb):
|
||||
# hopping[ik,isp,i,i] = R.next() * energy_unit
|
||||
#
|
||||
# # keep some things that we need for reading parproj:
|
||||
# things_to_set = ['n_shells','shells','n_corr_shells','corr_shells','n_spin_blocs','n_orbitals','n_k','SO','SP','energy_unit']
|
||||
# for it in things_to_set: setattr(self,it,locals()[it])
|
||||
# except StopIteration : # a more explicit error if the file is corrupted.
|
||||
# raise "Wien2k_converter : reading file %s failed!"%filename
|
||||
#
|
||||
# R.close()
|
||||
# # Reading done!
|
||||
|
||||
# Save it to the HDF:
|
||||
ar = HDFArchive(self.hdf_file,'a')
|
||||
|
|
|
|||
Loading…
Reference in New Issue
Block a user