analysis.rst done. Minor change in transport.rst

I also described how one can read a self energy form a data
        file. However, this needs to be tested and also included
        in the reference manual. Maybe the function should move
        back into sumk_dft_tools!?

doc/guide/analysis.rst

@@ -7,13 +7,13 @@ This section explains how to use some tools of the package in order to analyse t
 
 There are two practical tools for which a self energy on the real axis is not needed, namely:
 
-  * :meth:`dos_wannier_basis` for the density of states of the Wannier orbitals and
+  * :meth:`dos_wannier_basis <pytriqs.applications.dft.sumk_dft_tools.dos_wannier_basis>` for the density of states of the Wannier orbitals and
-  * :meth:`partial_charges` for the partial charges according to the Wien2k definition.
+  * :meth:`partial_charges <pytriqs.applications.dft.sumk_dft_tools.partial_charges>` for the partial charges according to the Wien2k definition.
 
 However, a real frequency self energy has to be provided by the user to use the methods:
 
-  * :meth:`dos_parproj_basis` for the momentum-integrated spectral function including self energy effects and
+  * :meth:`dos_parproj_basis <pytriqs.applications.dft.sumk_dft_tools.dos_parproj_basis>` for the momentum-integrated spectral function including self energy effects and
-  * :meth:`spaghettis` for the momentum-resolved spectral function (i.e. ARPES)
+  * :meth:`spaghettis <pytriqs.applications.dft.sumk_dft_tools.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
@@ -21,10 +21,6 @@ However, a real frequency self energy has to be provided by the user to use the
   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!
 
-.. note::
-  Add the doc for loading the self energy from a data file. We have to provide this option, because
-  in general the user won't has it stored in h5 file!!
-
 Initialisation
 --------------
 
@@ -40,16 +36,38 @@ class::
 
 Note that all routines available in :class:`SumkDFT` are also available here. 
 
-If required, a self energy is load and initialise in the next step. Most conveniently, 
+If required, we have to load and initialise the real frequency self energy. Most conveniently, 
-your self energy is already stored as a real frequency :class:`BlockGf` object 
+you have your self energy already stored as a real frequency :class:`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 we provide the function
+:meth:`constr_Sigma_real_axis`, which loads the data and puts it into a real frequency :class:`BlockGf` object::
+
+  from pytriqs.applications.dft.build_sigma_from_txt import *
+  SigmaReFreq = constr_Sigma_real_axis(SK, filename, hdf=False, hdf_dataset='SigmaReFreq',n_om=0, orb=0)
+
+where:
+ 
+  * `filename`: the name of the hdf5 archive file or the `fname` pattern in text files names as described above,  
+  * `hdf`: if `True`, the real axis self energy will be read from the hdf5 file, otherwise from the text files,
+  * `hdf_dataset`: the name of dataset where the self energy is stored in the hdf5 file,
+  * `orb`: index of an inequivalent shell,
+  * `n_om`: the number of points in the real-axis mesh (used only if `hdf=False`).
+
+
+It is important that some rules concerning the structure of the data is followed:
+  * Each data file should contain the three columns: real frequency, real part and imaginary part of the self-energy in exactly this order. 
+  * If all blocks of your self energy are of dimension 1x1, you store them in `filename_(block)0.dat` files. Here `(block)` is a block name (`up`, `down`, or combined `ud`). 
+  * In the case when you have matrix blocks, you store them in `(i)_(j).dat` files, where `(i)` and `(j)` are the zero based orbital indices, in the `filename_(block)` directory. 
+  
+Finally, we put the self energy into the `SK` object::  
+  
     SK.put_Sigma(Sigma_imp = [SigmaReFreq])
 
-Additionally, the chemical potential and the double counting
+and additionally set the chemical potential and the double counting correction from the DMFT calculation::
-correction from the DMFT calculation are set, and the archive is closed again::
   
   chemical_potential, dc_imp, dc_energ = SK.load(['chemical_potential','dc_imp','dc_energ'])
   SK.set_mu(chemical_potential)
@@ -65,8 +83,18 @@ 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 
+`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`.
+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 seperately for, e.g., :math:`d_{xy}`, :math:`d_{x^2-y^2}`, and so on,
+
+otherwise, the ouptut is returend by the function for further use in python.
 
 Partial charges
 ---------------
@@ -75,7 +103,7 @@ Since we can calculate the partial charges directly from the Matsubara Green's f
 real frequency self energy for this purpose. The calculation is done by::
 
   SK.put_Sigma(Sigma_imp = SigmaImFreq)
-  dm = SK.partial_charges(beta=40.0 with_Sigma=True, with_dc=True)
+  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
@@ -85,29 +113,24 @@ in the hdf5 archive. For the detailed structure of `dm`, see the reference manua
 Correlated spectral function (with real frequency self energy)
 --------------------------------------------------------------
 
-With this self energy, we can now execute::
+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=broadening)
+  SK.dos_parproj_basis(broadening=0.0, with_Sigma=True, with_dc=True, save_to_file=True)
 
-This produces both the momentum-integrated (total density of states or DOS) and orbitally-resolved (partial/projected DOS) spectral functions.
+The variable `broadening` is an additional Lorentzian broadening (default: `0.01 eV`) applied to the resulting spectra.
-The variable `broadening` is an additional Lorentzian broadening applied to the resulting spectra.
+The output is written in the same way as described above for Wannier density of states, but with file names 
-The output is printed into the files
+`DOS_parproj_*` instead.  
-
-  * `DOScorr(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.
-  * `DOScorr(sp)_proj(i).dat`: The DOS projected to an orbital with index `(i)`. The index `(i)` refers to 
-    the indices given in ``SK.shells``.
-  * `DOScorr(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 seperately for, e.g., :math:`d_{xy}`, :math:`d_{x^2-y^2}`, and so on.
 
 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. We assume here that we already converted the output of the :program:`dmftproj` program with the 
+experiments. First we have to execute `lapw1`, `lapw2 -almd` and :program:`dmftproj` with the `-band` 
-converter routines (see :ref:`conversion`). The spectral function is calculated by::
+option and use the :meth:`convert_bands_input()` routine to convert the required files. For a detailed description 
+see :ref:`conversion`. The spectral function is then calculated by::
 
-  SK.spaghettis(broadening)
+  SK.spaghettis(broadening=0.01,plot_shift=0.0,plot_range=None,ishell=None,save_to_file='Akw_')
 
 Optional parameters are
 

doc/guide/transport.rst

@@ -81,6 +81,8 @@ First we have to read the Wien2k files and store the relevant information in the
 
     SK = SumkDFTTools(hdf_file='case.h5', use_dft_blocks=True)
 
+The converter :meth:`convert_transport_input <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>` 
+reads the required data of the Wien2k output and stores it in the `dft_transp_input` subgroup of your hdf file. 
 Additionally we need to read and set the self energy, the chemical potential and the double counting::
 
     ar = HDFArchive('case.h5', 'a')