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analysis.rst half done and some other minor changes

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Manuel Zingl 2015-08-17 19:08:05 +02:00
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136
doc/guide/analysis.rst
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@ -3,75 +3,33 @@
Tools for analysis
==================
.. warning::
TO BE UPDATED!
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` for the density of states of the Wannier orbitals and
* :meth:`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:`spaghettis` for the momentum-resolved spectral function (i.e. ARPES)
.. warning::
The 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 frequancy axis!
There are methods included e.g. in the :program:`ALPS` package, which can be used for these purposes. But
be careful: All these methods have to be used very carefully!
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!
The tools for analysis can be found in an extension of the :class:`SumkDFT` class and are
loaded by importing the module :class:`SumkDFTTools`::
Most conveniently, you have your self energy already stored as a real frequency :class:`BlockGf` object
in a hdf5 file, which can be easily loaded::
from pytriqs.applications.dft.sumk_dft_tools import *
There are two practical tools for which you do not need a self energy on the real axis, namely the:
* density of states of the Wannier orbitals,
* partial charges according to the Wien2k definition.
The self energy on the real frequency axis is necessary in computing the:
* momentum-integrated spectral function including self-energy effects,
* momentum-resolved spectral function (i.e. ARPES).
The initialisation of the class is equivalent to that of the :class:`SumkDFT`
class::
SK = SumkDFTTools(hdf_file = filename)
Note that all routines available in :class:`SumkDFT` are also available here.
Routines without real-frequency self energy
-------------------------------------------
For plotting the
density of states of the Wannier orbitals, you simply type::
SK.check_input_dos(om_min, om_max, n_om)
which produces plots between the real frequencies `om_min` and `om_max`, using a mesh of `n_om` points. There
is an optional parameter `broadening` which defines an additional Lorentzian broadening, and has the default value of
`0.01` by default.
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::
ar = HDFArchive(SK.hdf_file)
SK.put_Sigma([ ar['SigmaImFreq'] ])
ar = HDFArchive(filename+'.h5','r')
SigmaReFreq = ar['SigmaReFreq']
del ar
dm = SK.partial_charges()
which calculates the partial charges using the data stored in the hdf5 file, namely the self energy, double counting, and
chemical potential. Here we assumed that the final self energy is stored as `SigmaImFreq` in the archive.
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 Wien2k converter routines and stored automatically
in the hdf5 archive. For the detailed structure of `dm`, see the reference manual.
Routines with real-frequency self energy
----------------------------------------
In order to plot data including correlation effects on the real axis, one has to provide the real frequency self energy.
Most conveniently, it is stored as a real frequency :class:`BlockGf` object in the hdf5 file::
ar = HDFArchive(filename+'.h5','a')
ar['SigmaReFreq'] = SigmaReFreq
del ar
.. note::
What happens if one has a self energy only in text files...?
You may also store it in text files. If all blocks of your self energy are of dimension 1x1, you store them in `fname_(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 orbital indices, in the `fname_(block)` directory.
@ -88,6 +46,57 @@ where:
The chemical potential as well as the double counting correction were already read in the initialisation process.
Initialisation
--------------
All tools described below are collected in an extension of the :class:`SumkDFT` class and are
loaded by importing the module :class:`SumkDFTTools`::
from pytriqs.applications.dft.sumk_dft_tools import *
The initialisation of the class is equivalent to that of the :class:`SumkDFT`
class::
SK = SumkDFTTools(hdf_file = filename + '.h5')
Note that all routines available in :class:`SumkDFT` are also available here.
If required, the real frequency self energy is set with::
SK.put_Sigma(Sigma_imp = [ SigmaReFreq ])
Density of states of the Wannier orbitals
-----------------------------------------
For plotting the
density of states of the Wannier orbitals, you simply type::
SK.check_input_dos(om_min, om_max, n_om)
which produces plots between the real frequencies `om_min` and `om_max`, using a mesh of `n_om` points. There
is an optional parameter `broadening` which defines an additional Lorentzian broadening, and has the default value of
`0.01` by default.
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::
ar = HDFArchive(SK.hdf_file)
SK.put_Sigma([ ar['SigmaImFreq'] ])
del ar
dm = SK.partial_charges()
which calculates the partial charges using the data stored in the hdf5 file, namely the self energy, double counting, and
chemical potential. Here we assumed that the final self energy is stored as `SigmaImFreq` in the archive.
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 Wien2k converter routines and stored automatically
in the hdf5 archive. For the detailed structure of `dm`, see the reference manual.
Correlated spectral function (with self energy)
-----------------------------------------------
With this self energy, we can now execute::
SK.dos_partial(broadening=broadening)
@ -103,6 +112,9 @@ The output is printed into the files
* `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 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
converter routines (see :ref:`interfacetowien`). The spectral function is calculated by::

4
doc/guide/conversion.rst
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@ -133,6 +133,10 @@ After this step, all the necessary information for the DMFT loop is
stored in the hdf5 archive, where the string variable
`Converter.hdf_filename` gives the file name of the archive.
At this point you should use the method :meth:`dos_wannier_basis`
contained in the module :class:`SumkDFTTools` to check the density of
states of the Wannier orbitals (see :ref:`analysis`).
You have now everything for performing a DMFT calculation, and you can
proceed with :ref:`singleshot`.

2
doc/guide/dftdmft_singleshot.rst
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@ -18,7 +18,7 @@ Before doing the calculation, we have to intialize all the objects that we will
to get the local quantities used in DMFT. It is initialized by::
from pytriqs.applications.dft.sumk_dft import *
SK = SumkDFT(hdf_file = filename)
SK = SumkDFT(hdf_file = filename + '.h5')
Setting up the impurity solver

10
doc/guide/transport.rst
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@ -36,9 +36,13 @@ Prerequisites
First perform a standard :ref:`DFT+DMFT calculation <dftdmft_selfcons>` for your desired material and obtain the real-frequency self energy by doing an
analytic continuation.
.. note::
It is crucial to perform the analytic continuation in such a way that the obtained real-frequency self energy is accurate around the Fermi energy as only its
low energy structure influences the final results!
.. warning::
This package does NOT provide an explicit method to do an **analytic continuation** of
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. Especially for optics calculations
it is crucial to perform the analytic continuation in such a way that the obtained real frequency self energy
is accurate around the Fermi energy as low energy features strongly influence the final results!
Besides the self energy the Wien2k files read by the transport converter (:meth:`convert_transport_input <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>`) are:
* :file:`.struct`: The lattice constants specified in the struct file are used to calculate the unit cell volume.