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dft_tools/doc/reference/h5structure.rst
2015-08-13 15:27:50 +02:00

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.. _hdfstructure:
hdf5 structure
==============
All the data is stored using the hdf5 standard, as described also in the
documentation of the TRIQS package itself. In order to do a DMFT calculation,
using input from DFT applications, a converter is needed on order to provide
the necessary data in the hdf5 format.
groups and their formats
------------------------
In order to be used with the DMFT routines, the following data needs to be
provided in the hdf5 file. It contains a lot of information in order to perform
DMFT calculations for all kinds of situations, e.g. d-p Hamiltonians, more than
one correlated atomic shell, or using symmetry operations for the k-summation.
We store all data in subgroups of the hdf5 archive:
Main data
^^^^^^^^^
There needs to be one subgroup for the main data of the
calculation. The default name of this group is `dft_input`. Its contents are
================= ====================================================================== =====================================================================================
Name Type Meaning
================= ====================================================================== =====================================================================================
energy_unit numpy.float Unit of energy used for the calculation.
n_k numpy.int Number of k-points used for the BZ integration.
k_dep_projection numpy.int 1 if the dimension of the projection operators depend on the k-point,
0 otherwise.
SP numpy.int 1 for spin-polarised Hamiltonian, 0 for paramagnetic Hamiltonian.
SO numpy.int 1 if spin-orbit interaction is included, 0 otherwise.
charge_below numpy.float Number of electrons in the crystal below the correlated orbitals.
Note that this is for compatibility with dmftproj.
density_required numpy.float Required total electron density. Needed to determine the chemical potential.
The density in the projection window is then `density_required`-`charge_below`.
symm_op numpy.int 1 if symmetry operations are used for the BZ sums,
0 if all k-points are directly included in the input.
n_shells numpy.int Number of atomic shells for which post-processing is possible.
Note: this is `not` the number of correlated orbitals!
If there are two equivalent atoms in the unit cell, `n_shells` is 2.
shells list of dict {string:int}, dim n_shells x 4 Atomic shell information.
For each shell, have a dict with keys ['atom', 'sort', 'l', 'dim'].
'atom' is the atom index, 'sort' defines the equivalency of the atoms,
'l' is the angular quantum number, 'dim' is the dimension of the atomic shell.
e.g. for two equivalent atoms in the unit cell, `atom` runs from 0 to 1,
but `sort` can take only one value 0.
n_corr_shells numpy.int Number of correlated atomic shells.
If there are two correlated equivalent atoms in the unit cell, `n_corr_shells` is 2.
corr_shells list of dict {string:int}, dim n_corr_shells x 6 Correlated orbital information.
For each correlated shell, have a dict with keys
['atom', 'sort', 'l', 'dim', 'SO', 'irep'].
'atom' is the atom index, 'sort' defines the equivalency of the atoms,
'l' is the angular quantum number, 'dim' is the dimension of the atomic shell.
'SO' is one if spin-orbit is included, 0 otherwise, 'irep' is a dummy integer 0.
use_rotations numpy.int 1 if local and global coordinate systems are used, 0 otherwise.
rot_mat list of numpy.array.complex, Rotation matrices for correlated shells, if `use_rotations`.
dim n_corr_shells x [corr_shells['dim'],corr_shells['dim']] Set to the unity matrix if no rotations are used.
rot_mat_time_inv list of numpy.int, dim n_corr_shells If `SP` is 1, 1 if the coordinate transformation contains inversion, 0 otherwise.
If `use_rotations` or `SP` is 0, give a list of zeros.
n_reps numpy.int Number of irreducible representations of the correlated shell.
e.g. 2 if eg/t2g splitting is used.
dim_reps list of numpy.int, dim n_reps Dimension of the representations.
e.g. [2,3] for eg/t2g subsets.
T list of numpy.array.complex, Transformation matrix from the spherical harmonics to impurity problem basis
dim n_inequiv_corr_shell x normally the real cubic harmonics).
[max(corr_shell['dim']),max(corr_shell['dim'])] This matrix is used to calculate the 4-index U matrix.
n_orbitals numpy.array.int, dim [n_k,SP+1-SO] Number of Bloch bands included in the projection window for each k-point.
If SP+1-SO=2, the number of included bands may depend on the spin projection up/down.
proj_mat numpy.array.complex, Projection matrices from Bloch bands to Wannier orbitals.
dim [n_k,SP+1-SO,n_corr_shells,max(corr_shell['dim']),max(n_orbitals)] For efficient storage reasons, all matrices must be of the same size
(given by last two indices).
For k-points with fewer bands, only the first entries are used, the rest are zero.
e.g. if number of Bloch bands ranges from 4-6, all matrices are of size 6.
bz_weights numpy.array.float, dim n_k Weights of the k-points for the k summation.
hopping numpy.array.complex, Non-interacting Hamiltonian matrix for each k point.
dim [n_k,SP+1-SO,max(n_orbitals),max(n_orbitals)] As for `proj_mat`, all matrices have to be of the same size.
================= ====================================================================== =====================================================================================
Symmetry operations
^^^^^^^^^^^^^^^^^^^
In this subgroup we store all the data for applying the symmetry operations in
the DMFT loop (in case you want to use symmetry operations). The default name
of this subgroup is `dft_symmcorr_input`. This information is needed only if symmetry
operations are used to do the k summation. To be continued...
.. warning::
TO BE COMPLETED!
General and simple H(k) Converter
---------------------------------
The above described converter of the Wien2k input is quite involved, since
Wien2k provides a lot of information, e.g. about symmetry operations, that can
be used in the calculation. However, sometimes we want to use a light
implementation where the input consists basically only of the Hamiltonian
matrix in Wannier basis, given at a grid of k points in the first Brillouin
zone. For this purpose, a simple converter is included in the package, called
:class:`HkConverter`, which is implemented for the simplest case of
paramagnetic DFT calculations without spin-orbit coupling. It reads a simple,
easy to construct text file, and produces an archive that can be used for the
DMFT calculations. An example input file for a structure with one correlated
site with 3 t2g orbitals in the unit cell contains the following:
10 <- n_k
1.0 <- density_required
1 <- n_shells
1 1 2 3 <- shells, as above: atom, sort, l, dim
1 <- n_corr_shells
1 1 2 3 0 0 <- corr_shells, as above: atom, sort, l, dim, SO, dummy
2 2 3 <- n_reps, dim_reps (length 2, because eg/t2g splitting) for each inequivalent correlated shell
After this header, we give the Hamiltonian matrices for al the k-points. for
each k-point we give first the matrix of the real part, then the matrix of the
imaginary part. The projection matrices are set automatically to unity
matrices, no rotations, no symmetry operations are used. That means that the
symmetry sub group in the hdf5 archive needs not be set, since it is not used.
It is furthermore assumed that all k-points have equal weight in the k-sum.
Note that the input file should contain only the numbers, not the comments
given in above example.
The Hamiltonian matrices can be taken, e.g., from Wannier90, which contructs
the Hamiltonian in a maximally localised Wannier basis.
Note that with this simplified converter, no full charge self consistent
calculations are possible!