dft_tools/doc/guide/analysis.rst

.. _analysis:

Tools for analysis
==================

This section explains how to use some tools of the package in order to analyse the data.

There are two practical tools for which a self energy on the real axis is not needed, namely:

  * :meth:`dos_wannier_basis <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.dos_wannier_basis>` for the density of states of the Wannier orbitals and
  * :meth:`partial_charges <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.partial_charges>` for the partial charges according to the :program:`Wien2k` definition.

However, a real frequency self energy has to be provided by the user for the methods:

  * :meth:`dos_parproj_basis <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.dos_parproj_basis>` for the momentum-integrated spectral function including self energy effects and
  * :meth:`spaghettis <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.spaghettis>` for the momentum-resolved spectral function (i.e. ARPES)

.. warning::
  This package does NOT provide an explicit method to do an **analytic continuation** of the
  self energies and Green functions from Matsubara frequencies to the real frequency axis! 
  There are methods included e.g. in the :program:`ALPS` package, which can be used for these purposes. 
  Keep in mind that all these methods have to be used very carefully!

Initialisation
--------------

All tools described below are collected in an extension of the :class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` class and are
loaded by importing the module :class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>`::

  from pytriqs.applications.dft.sumk_dft_tools import *

The initialisation of the class is equivalent to that of the :class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` 
class::

  SK = SumkDFTTools(hdf_file = filename + '.h5')

Note that all routines available in :class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` are also available here. 

If required, we have to load and initialise the real frequency self energy. Most conveniently, 
you have your self energy already stored as a real frequency :class:`BlockGf <pytriqs.gf.local.BlockGf>` object 
in a hdf5 file::

  ar = HDFArchive('case.h5', 'a')
  SigmaReFreq = ar['dmft_output']['Sigma_w']

You may also have your self energy stored in text files. For this case the :ref:`TRIQS <triqslibs:welcome>` library offers 
the function :meth:`read_gf_from_txt`, which is able to load the data from text files of one Greens function block
into a real frequency :class:`ReFreqGf <pytriqs.gf.local.ReFreqGf>` object. Loading each block separately and
building up a :class:´BlockGf <pytriqs.gf.local.BlockGf>´ is done with::

  from pytriqs.gf.local.tools import *
  # get block names
  n_list = [n for n,nl in SK.gf_struct_solver[0].iteritems()]
  # load sigma for each block - in this example sigma is composed of 1x1 blocks
  g_blocks = [read_gf_from_txt(block_txtfiles=[['Sigma_'+name+'.dat']], block_name=n) for n in n_list]
  # put the data into a BlockGf object
  SigmaReFreq = BlockGf(name_list=n_list, block_list=g_blocks, make_copies=False)

where:
 
  * `block_txtfiles` is a rank 2 square np.array(str) or list[list[str]] holding the file names of one block and 
  * `block_name` is the name of the block.

It is important that each data file has to contain three columns: the real frequency mesh, the real part and the imaginary part
of the self energy - exactly in this order! The mesh should be the same for all files read in and non-uniform meshes are not supported. 
  
Finally, we set the self energy into the `SK` object::  
  
    SK.set_Sigma([SigmaReFreq])

and additionally set the chemical potential and the double counting correction from the DMFT calculation::
  
  chemical_potential, dc_imp, dc_energ = SK.load(['chemical_potential','dc_imp','dc_energ'])
  SK.set_mu(chemical_potential)
  SK.set_dc(dc_imp,dc_energ)
  del ar

.. _dos_wannier:

Density of states of the Wannier orbitals
-----------------------------------------

For plotting the density of states of the Wannier orbitals, you type::

  SK.dos_wannier_basis(broadening=0.03, mesh=[om_min, om_max, n_om], with_Sigma=False, with_dc=False, save_to_file=True)

which produces plots between the real frequencies `om_min` and `om_max`, using a mesh of `n_om` points. The parameter 
`broadening` defines an additional Lorentzian broadening, and has the default value of `0.01 eV`. To check the Wannier 
density of states after the projection set `with_Sigma` and `with_dc` to `False`. If `save_to_file` is set to `True`
the output is printed into the files

  * `DOS_wannier_(sp).dat`: The total DOS, where `(sp)` stands for `up`, `down`, or combined `ud`. The latter case
    is relevant for calculations including spin-orbit interaction.
  * `DOS_wannier_(sp)_proj(i).dat`: The DOS projected to an orbital with index `(i)`. The index `(i)` refers to 
    the indices given in ``SK.shells``.
  * `DOS_wannier_(sp)_proj(i)_(m)_(n).dat`: As above, but printed as orbitally-resolved matrix in indices 
    `(m)` and `(n)`. For `d` orbitals, it gives the DOS separately for, e.g., :math:`d_{xy}`, :math:`d_{x^2-y^2}`, and so on,

otherwise, the output is returned by the function for a further usage in :program:`python`.

Partial charges
---------------

Since we can calculate the partial charges directly from the Matsubara Green's functions, we also do not need a
real frequency self energy for this purpose. The calculation is done by::

  SK.set_Sigma(SigmaImFreq)
  dm = SK.partial_charges(beta=40.0, with_Sigma=True, with_dc=True)

which calculates the partial charges using the self energy, double counting, and chemical potential as set in the 
`SK` object. On return, `dm` is a list, where the list items correspond to the density matrices of all shells
defined in the list `SK.shells`. This list is constructed by the :program:`Wien2k` converter routines and stored automatically
in the hdf5 archive. For the structure of `dm`, see also :meth:`reference manual <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.partial_charges>`.

Correlated spectral function (with real frequency self energy)
--------------------------------------------------------------

To produce both the momentum-integrated (total density of states or DOS) and orbitally-resolved (partial/projected DOS) spectral functions
we can execute::
  
  SK.dos_parproj_basis(broadening=0.0, with_Sigma=True, with_dc=True, save_to_file=True)

The variable `broadening` is an additional Lorentzian broadening (default: `0.01 eV`) applied to the resulting spectra.
The output is written in the same way as described above for the :ref:`Wannier density of states <dos_wannier>`, but with filenames 
`DOS_parproj_*` instead.  

Momentum resolved spectral function (with real frequency self energy)
---------------------------------------------------------------------

Another quantity of interest is the momentum-resolved spectral function, which can directly be compared to ARPES
experiments. First we have to execute `lapw1`, `lapw2 -almd` and :program:`dmftproj` with the `-band` 
option and use the :meth:`convert_bands_input <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter.convert_bands_input>`
routine, which converts the required files (for a more detailed description see :ref:`conversion`). The spectral function is then calculated by typing::

  SK.spaghettis(broadening=0.01,plot_shift=0.0,plot_range=None,ishell=None,save_to_file='Akw_')

Here, optional parameters are

  * `shift`: An additional shift added as `(ik-1)*shift`, where `ik` is the index of the `k` point. This is useful for plotting purposes. 
    The default value is 0.0.
  * `plotrange`: A list with two entries, :math:`\omega_{min}` and :math:`\omega_{max}`, which set the plot
    range for the output. The default value is `None`, in which case the full momentum range as given in the self energy is used. 
  * `ishell`: An integer denoting the orbital index `ishell` onto which the spectral function is projected. The resulting function is saved in 
    the files. The default value is `None`. Note for experts: The spectra are not rotated to the local coordinate system used in :program:`Wien2k`.

The output is written as the 3-column files ``Akw(sp).dat``, where `(sp)` is defined as above. The output format is 
`k`, :math:`\omega`, `value`.