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6
doc/about.rst
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@ -14,14 +14,16 @@ Olivier Parcollet (CEA Saclay). A first step has been the definition of the
framework and the construction of the projective Wannier functions as input for
the DMFT calculations [#dft_tools1]_. This has been followed by the introduction
of full charge self-consistency [#dft_tools2]_, necessary for total energy
calculations.
calculations. The package at hand is fully implemented as an application
based on the TRIQS library [#dft_tools3]_.
**Developers**: M. Aichhorn, L. Pourovskii, V. Vildosola, C. Martins, P. Seth, M. Zingl
**Developers**: M. Aichhorn, L. Pourovskii, P.Seth, V. Vildosola, M. Zingl, O. E. Peil, X. Deng, J. Mravlje, G. Kraberger, C. Martins, M. Ferrero, O. Parcollet
**Related papers**:
.. [#dft_tools1] `M. Aichhorn, L. Pourovskii, V. Vildosola, M. Ferrero, O. Parcollet, T. Miyake, A. Georges, and S. Biermann, Phys. Rev. B 80, 085101 (2009) <http://link.aps.org/doi/10.1103/PhysRevB.80.085101>`_ (:download:`bibtex file <dft_tools1.bib>`)
.. [#dft_tools2] `M. Aichhorn, L. Pourovskii, and A. Georges, Phys. Rev. B 84, 054529 (2011) <http://link.aps.org/doi/10.1103/PhysRevB.84.054529>`_ (:download:`bibtex file <dft_tools2.bib>`)
.. [#dft_tools3] `M. Aichhorn, L. Pourovskii, P.Seth, V. Vildosola, M. Zingl, O. E. Peil, X. Deng, J. Marvlje, G. Kraberger, C. Martins, M. Ferrero, and O. Parcollet, Commt. Phys. Commun. 204, 200 (2016) <http://www.sciencedirect.com/science/article/pii/S0010465516300728>`_ (:download:`bibtex file <dft_tools3.bib>`)
This application is a part of our scientific work and we would appreciate if
projects using it will include a citation to the above relevant papers. In

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@ -1,3 +1,5 @@
.. _dftplusdmft:
Introduction to DFT+DMFT
========================
@ -8,7 +10,7 @@ terms it states that electrons in a crystal form bands of allowed
states in momentum space. These states are then filled by the
electrons according to Pauli's principle up the Fermi level. With this
simple picture one can explain the electronic band structure of simple
materials such as elementary copper or aluminium.
materials such as elementary copper or aluminum.
Following this principle one can easily classify all existing
materials into metals and insulators, with semiconductors being
@ -17,9 +19,8 @@ spectrum. Following this band theory, a system is a metal if there is
an odd number of electrons in the valence bands, since this leads to a
partially filled band, cutting the Fermi energy and, thus, producing a
Fermi surface, i.e metallic behavior. On the other hand, an even
number of electrons leads to
completely filled bands with a finite excitation gap to the conduction
bands, i.e. insulating behavior.
number of electrons leads to completely filled bands with a finite
excitation gap to the conduction bands, i.e. insulating behavior.
This classification works pretty well for a large class of
materials, where the electronic band structures are reproduced by
@ -41,7 +42,7 @@ current
because of the strong Coulomb repulsion between the electrons. With
reference to Sir Nevill Mott, who contributed substantially to the
explanation of this effect in the 1930's, these materials are in
general reffered to as Mott insulators.
general referred to as Mott insulators.
Density-functional theory in a (very small) nutshell
----------------------------------------------------
@ -63,7 +64,7 @@ that is discussed in the literature on DFT, let us just note that the
main result of DFT calculations are the Kohn-Sham energies
:math:`\varepsilon_{\nu\mathbf{k}}` and the Kohn-Sham orbitals :math:`\psi_{\nu\mathbf{k}}(\mathbf{r})`.
This set of equations is exact, however, the exchange correlation
potential :math:`V_{xc}(\mathbf{r})` is not known explicitely. In
potential :math:`V_{xc}(\mathbf{r})` is not known explicitly. In
order to do actual calculations, it needs to be approximated in some
way. The local density approximation is one of the most famous
approximations used in this context. This approximation works well for
@ -75,7 +76,7 @@ From DFT to DMFT
In order to extend our calculations to strong correlations, we need to
go from a description by bands to a description in terms of
(localised) orbitals: Wannier functions.
(localized) orbitals: Wannier functions.
In principle, Wannier functions :math:`\chi_{\mu\sigma}(\mathbf{r})`
are nothing else than a Fourier transform of the Bloch basis set from
@ -88,7 +89,7 @@ where we introduced also the spin degree of freedom :math:`\sigma`. The
unitary matrix :math:`U_{\mu\nu}` is not uniquely defined, but allows for a
certain amount of freedom in the calculation of Wannier function. A
very popular choice is the constraint that the resulting Wannier
functions should be maximally localised in space. Another route,
functions should be maximally localized in space. Another route,
computationally much lighter and more stable, are projective Wannier
functions. This scheme is used for the Wien2k interface in this
package.
@ -98,7 +99,7 @@ A central quantity in this scheme is the projection operator
:math:`\nu` a Bloch band index.
Its definition and how it is calculated can be found in the original
literature or in the extensive documentation of the
:program:`dmftproj` program shipped with :program:`dft_tools`.
:program:`dmftproj` program shipped with :program:`DFTTools`.
Using projective Wannier functions for DMFT
-------------------------------------------
@ -121,7 +122,7 @@ with the DFT Green function
This non-interacting Green function :math:`G^0_{mn}(i\omega)` defines,
together with the interaction Hamiltonian, the Anderson impurity
model. The DMFT self-consitency cycle can now be formulated as
model. The DMFT self-consistency cycle can now be formulated as
follows:
#. Take :math:`G^0_{mn}(i\omega)` and the interaction Hamiltonian and
@ -173,9 +174,9 @@ Full charge self-consistency
The feedback of the electronic correlations to the Kohn-Sham orbitals
is included by the interacting density matrix. With going into the
details, it basically consists of calculating the Kohn Sham density
details, it basically consists of calculating the Kohn-Sham density
:math:`\rho(\mathbf{r})` in the presence of this interacting density
matrix. This new density now defines a new Kohn Sham
matrix. This new density now defines a new Kohn-Sham
exchange-correlation potential, which in turn leads to new
:math:`\varepsilon_{\nu\mathbf{k}}`,
:math:`\psi_{\nu\mathbf{k}}(\mathbf{r})`, and projectors
@ -186,4 +187,4 @@ step 3, before the local lattice Green
function is downfolded again into orbital space.
How all these calculations can be done in practice with this
:program:`dft_tools` package is subject of the user guide in this documentation.
:program:`DFTTools` package is subject of the user guide in this documentation.

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@ -0,0 +1,72 @@
What you should know
====================
Probably, you can hardly wait to perform your first DFT+DMFT calculation
with the :program:`DFTTools` package. This documentation and user guide
should make it as easy as possible to get started quickly.
However, it is mutually important to sort out a few prerequisites first.
What is :program:`DFTTools`?
----------------------------
:program:`DFTTools` connects the :ref:`TRIQS <triqslibs:welcome>` library
to realistic materials calculations based
on density functional theory (DFT). It allows an efficient implementation
of DFT plus dynamical mean-field theory (DMFT) calculations and it supplies
tools and methods to construct Wannier functions and to perform the
DMFT self-consistency cycle in this basis set. Post-processing tools,
such as band-structure plotting or the calculation of transport properties
are also implemented. The package comes with a fully charge self-consistent
interface to the Wien2k band structure code, as well as a generic interface.
We assume that you are already know about DFT and the usage of Wien2k.
Have a look at :ref:`DFT+DMFT page <dftplusdmft>` for a brief introduction on
the DFT+DMFT method and on how the theory is reflected in the
:ref:`basic structure <structure>` of the :program:`DFTTools` package.
Understand the philosophy of :program:`DFTTools`
------------------------------------------------
The purpose of :program:`DFTTools` is to provide the necessary tools
required for a DFT+DMFT calculations. Putting those tools together to a working
DFT+DMFT implementation is the task of the user. We do not
supply an universal script which runs with the click of a button, simply because
each material requires a different treatment or different settings.
Building your own script offers a great deal of flexibility and customizability.
Additionally, the :ref:`DFTTools user guide <documentation>` is there to support you
during this process.
It should go without saying, but the verification of outputs and the inspection
of results on their meaningfulness is the responsibility of the user.
The :program:`DFTTools` package is a toolbox and **not** a black box!
Learn how to use :ref:`TRIQS <triqslibs:welcome>` (and the :ref:`CTHYB <triqscthyb:welcome>` solver)
----------------------------------------------------------------------------------------------------
As :program:`DFTTools` is a :ref:`TRIQS <triqslibs:welcome>` based application
it is beneficial to invest a few hours to become familiar with
the :ref:`TRIQS <triqslibs:welcome>` basics first. The
:ref:`TRIQS tutorial <triqslibs:tutorials>` covers
the most important aspects of :ref:`TRIQS <triqslibs:welcome>`. We recommend
downloading our hands-on training in the form of ipython notebooks from
the `tutorials repository on GitHub <https://github.com/TRIQS/tutorials>`_.
Tutorials 1 to 6 are on the :ref:`TRIQS <triqslibs:welcome>` library, whereas tutorials
7 and 8 are more specific to the usage of the :ref:`CTHYB <triqscthyb:welcome>`
hybridization-expansion solver. In general, those tutorials will take at least a full day to finish.
Afterwards you can continue with the :ref:`DFTTools user guide <documentation>`.
Maximum Entropy (MaxEnt)
------------------------
Analytic continuation is needed for many :ref:`post-processing tools <analysis>`, e.g. to
calculate the spectral function, the correlated band structure (:math:`A(k,\omega)`)
and to perform :ref:`transport calculations <Transport>`.
You can use the Pade approximation available in the :ref:`TRIQS <triqslibs:welcome>` library, however,
it turns out to be very unstable for noisy numerical data. Most of the time, the MaxEnt method
is used to obtain data on the real-frequency axis. At the moment neither :ref:`TRIQS <triqslibs:welcome>` nor
:program:`DFTTools` provide such routines.

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@ -1,18 +1,21 @@
Structure of DFT Tools
======================
.. _structure:
Structure of :program:`DFTTools`
================================
.. image:: images/structure.png
:width: 700
:align: center
The central part of :program:`dft_tools`, which is performing the
The central part of :program:`DFTTools`, which is performing the
steps for the DMFT self-consistency cycle, is written following the
same philosophy as the :ref:`TRIQS <triqslibs:welcome>` toolbox. At
the user level, easy-to-use python modules are provided that allow to
write simple and short scripts performing the actual
calculation. Here, we will describe the general structure of the
package, for the details of how to use the modules, please consult the
user guide of this :ref:`documentation`.
write simple and short scripts performing the actual calculation.
The usage of those modules is presented in the user guide of this
:ref:`documentation`. Before considering the user guide, we suggest
to read the following introduction on the general structure of
the :program:`DFTTools` package.
The interface layer
-------------------
@ -30,37 +33,37 @@ Wien2k interface
""""""""""""""""
This interface layer consists of two parts. First, the output from Wien2k
is taken, and localised Wannier orbitals are constructed. This is done
by the fortran program :program:`dmftproj`. The second part consist in
is taken, and localized Wannier orbitals are constructed. This is done
by the FORTRAN program :program:`dmftproj`. The second part consist in
the conversion of the :program:`dmftproj` into the hdf5 file
format to be used for the DMFT calculation. This step is done by a
python routine called :class:`Wien2kConverter`, that reads the text output and
creates the hdf5 input file with the necessary ingredients. Quite
naturally, :program:`dft_tools` will adopt this converter concept also for future
naturally, :program:`DFTTools` will adopt this converter concept also for future
developments for other DFT packages.
General interface
"""""""""""""""""
In addition to the specialised Wien2k interface, :program:`dft_tools`
In addition to the specialized Wien2k interface, :program:`DFTTools`
provides also a very light-weight general interface. It basically
consists of a very simple :class:`HkConverter`. As input it requires a
hamiltonian matrix :math:`H_{mn}(\mathbf{k})` written already in
localised-orbital indices :math:`m,n`, on a :math:`\mathbf{k}`-point
Hamiltonian matrix :math:`H_{mn}(\mathbf{k})` written already in
localized-orbital indices :math:`m,n`, on a :math:`\mathbf{k}`-point
grid covering the Brillouin zone, and just a few other informations
like total numer of electrons, how many correlated atoms in the unit
cell, and so on. It converts this hamiltonian into a hdf5 format and
like total number of electrons, how many correlated atoms in the unit
cell, and so on. It converts this Hamiltonian into a hdf5 format and
sets some variables to standard values, such that it can be used with
the python modules performing the DMFT calculation. How the
hamiltonian matrix :math:`H_{mn}(\mathbf{k})` is actually calculated,
is **not** part of this interace.
Hamiltonian matrix :math:`H_{mn}(\mathbf{k})` is actually calculated,
is **not** part of this interface.
The DMFT calculation
--------------------
As mentioned above, there are a few python routines that allow to
perform the multi-band DMFT calculation in the context of real
materials. The major part is contained inte module
materials. The major part is contained in the module
:class:`SumkDFT`. It contains routines to
* calculate local Greens functions
@ -69,7 +72,7 @@ materials. The major part is contained inte module
* calculate the double-counting correction
* calculate the chemical potential in order to get the electron count right
* other things like determining the structure of the local
hamiltonian, rotating from local to global coordinate systems, etc.
Hamiltonian, rotating from local to global coordinate systems, etc.
At the user level, all these routines can be used to construct
situation- and problem-dependent DMFT calculations in a very efficient
@ -90,8 +93,8 @@ Post-processing
The main result of DMFT calculation is the interacting Greens function
and the Self energy. However, one is normally interested in
quantitites like band structure, density of states, or transport
properties. In order to calculate these things, :program:`dft_tools`
quantities like band structure, density of states, or transport
properties. In order to calculate these things, :program:`DFTTools`
provides the post-processing modules :class:`SumkDFTTools`. It
contains routines to calculate
@ -102,11 +105,8 @@ contains routines to calculate
or thermopower.
.. warning::
At the moment neither :ref:`TRIQS<triqslibs:welcome>` nor :program:`dft_tools`
At the moment neither :ref:`TRIQS<triqslibs:welcome>` nor :program:`DFTTools`
provides Maximum Entropy routines! You can use the Pade
approximants implemented in the TRIQS library, or you use your own
approximation implemented in the :ref:`TRIQS <triqslibs:welcome>` library, or you use your own
home-made Maximum Entropy code to do the analytic continuation from
Matsubara to the real-frequency axis.

11
doc/conf.py.in
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@ -17,7 +17,7 @@ extensions = ['sphinx.ext.autodoc',
source_suffix = '.rst'
project = u'TRIQS_DFT Tools'
project = u'TRIQS DFTTools'
copyright = u'2011-2013, M. Aichhorn, L. Pourovskii, V. Vildosola, C. Martins'
version = '@DFT_TOOLS_VERSION@'
release = '@DFT_TOOLS_RELEASE@'
@ -28,16 +28,15 @@ templates_path = ['@CMAKE_SOURCE_DIR@/doc/_templates']
html_theme = 'triqs'
html_theme_path = ['@TRIQS_THEMES_PATH@']
html_show_sphinx = False
html_context = {'header_title': 'dft_tools',
'header_subtitle': 'connecting <a class="triqs" style="font-size: 12px" href="http://ipht.cea.fr/triqs">TRIQS</a> to DFT packages',
html_context = {'header_title': 'dft tools',
'header_subtitle': 'connecting <a class="triqs" style="font-size: 12px" href="http://triqs.ipht.cnrs.fr/1.x">TRIQS</a> to DFT packages',
'header_links': [['Install', 'install'],
['Documentation', 'documentation'],
['Issues', 'issues'],
['About dft_tools', 'about']]}
['About DFTTools', 'about']]}
html_static_path = ['@CMAKE_SOURCE_DIR@/doc/_static']
html_sidebars = {'index': ['sideb.html', 'searchbox.html']}
htmlhelp_basename = 'TRIQSDftToolsdoc'
intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'triqslibs': ('http://ipht.cea.fr/triqs', None),
'triqscthyb': ('http://ipht.cea.fr/triqs/applications/cthyb', None)}
intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'triqslibs': ('http://triqs.ipht.cnrs.fr/1.x', None), 'triqscthyb': ('https://triqs.ipht.cnrs.fr/1.x/applications/cthyb/', None)}

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@ -0,0 +1,13 @@
@Article{TRIQS/DFTTools,
title = "TRIQS/DFTTools: A \{TRIQS\} application for ab initio calculations of correlated materials ",
journal = "Computer Physics Communications ",
volume = "204",
number = "",
pages = "200 - 208",
year = "2016",
note = "",
issn = "0010-4655",
doi = "http://dx.doi.org/10.1016/j.cpc.2016.03.014",
url = "http://www.sciencedirect.com/science/article/pii/S0010465516300728",
author = "Markus Aichhorn and Leonid Pourovskii and Priyanka Seth and Veronica Vildosola and Manuel Zingl and Oleg E. Peil and Xiaoyu Deng and Jernej Mravlje and Gernot J. Kraberger and Cyril Martins and Michel Ferrero and Olivier Parcollet",
}

5
doc/documentation.rst
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@ -1,4 +1,4 @@
.. module:: pytriqs.applications.dft_tools
.. module:: pytriqs.applications.dft
.. _documentation:
@ -11,6 +11,7 @@ Basic notions
.. toctree::
:maxdepth: 2
basicnotions/first
basicnotions/dft_dmft
basicnotions/structure
@ -23,6 +24,7 @@ User guide
guide/conversion
guide/dftdmft_singleshot
guide/SrVO3
guide/dftdmft_selfcons
guide/analysis
guide/full_tutorial
@ -43,6 +45,7 @@ This is the reference manual for the python routines.
reference/sumk_dft_tools
reference/symmetry
reference/transbasis
reference/block_structure
FAQs

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@ -0,0 +1,224 @@
.. _SrVO3:
SrVO3 (single-shot)
===================
We will discuss now how to set up a full working calculation,
including the initialization of the :ref:`CTHYB solver <triqscthyb:welcome>`.
Some additional parameter are introduced to make the calculation
more efficient. This is a more advanced example, which is
also suited for parallel execution. The conversion, which
we assume to be carried out already, is discussed :ref:`here <conversion>`.
For the convenience of the user, we provide also two
working python scripts in this documentation. One for a calculation
using Kanamori definitions (:download:`dft_dmft_cthyb.py
<images_scripts/dft_dmft_cthyb.py>`) and one with a
rotational-invariant Slater interaction Hamiltonian (:download:`dft_dmft_cthyb_slater.py
<images_scripts/dft_dmft_cthyb.py>`). The user has to adapt these
scripts to his own needs.
Loading modules
---------------
First, we load the necessary modules::
from pytriqs.applications.dft.sumk_dft import *
from pytriqs.gf.local import *
from pytriqs.archive import HDFArchive
from pytriqs.operators.util import *
from pytriqs.applications.impurity_solvers.cthyb import *
The last two lines load the modules for the construction of the
:ref:`CTHYB solver <triqscthyb:welcome>`.
Initializing SumkDFT
--------------------
We define some parameters, which should be self-explanatory::
dft_filename = 'SrVO3' # filename
U = 4.0 # interaction parameters
J = 0.65
beta = 40 # inverse temperature
loops = 15 # number of DMFT loops
mix = 0.8 # mixing factor of Sigma after solution of the AIM
dc_type = 1 # DC type: 0 FLL, 1 Held, 2 AMF
use_blocks = True # use bloc structure from DFT input
prec_mu = 0.0001 # precision of chemical potential
And next, we can initialize the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` class::
SK = SumkDFT(hdf_file=dft_filename+'.h5',use_dft_blocks=use_blocks)
Initializing the solver
-----------------------
We also have to specify the :ref:`CTHYB solver <triqscthyb:welcome>` related settings.
We assume that the DMFT script for SrVO3 is executed on 16 cores. A sufficient set
of parameters for a first guess is::
p = {}
# solver
p["random_seed"] = 123 * mpi.rank + 567
p["length_cycle"] = 200
p["n_warmup_cycles"] = 100000
p["n_cycles"] = 1000000
# tail fit
p["perform_tail_fit"] = True
p["fit_max_moment"] = 4
p["fit_min_n"] = 30
p["fit_max_n"] = 60
Here we use a tail fit to deal with numerical noise of higher Matsubara frequencies.
For other options and more details on the solver parameters, we refer the user to
the :ref:`CTHYB solver <triqscthyb:welcome>` documentation.
It is important to note that the solver parameters have to be adjusted for
each material individually. A guide on how to set the tail fit parameters is given
:ref:`below <tailfit>`.
The next step is to initialize the
:class:`solver class <pytriqs.applications.impurity_solvers.cthyb.Solver>`.
It consist of two parts:
#. Calculating the multi-band interaction matrix, and constructing the
interaction Hamiltonian.
#. Initializing the solver class itself.
The first step is done using methods of the :ref:`TRIQS <triqslibs:welcome>` library::
n_orb = SK.corr_shells[0]['dim']
l = SK.corr_shells[0]['l']
spin_names = ["up","down"]
orb_names = [i for i in range(n_orb)]
# Use GF structure determined by DFT blocks:
gf_struct = SK.gf_struct_solver[0]
# Construct U matrix for density-density calculations:
Umat, Upmat = U_matrix_kanamori(n_orb=n_orb, U_int=U, J_hund=J)
We assumed here that we want to use an interaction matrix with
Kanamori definitions of :math:`U` and :math:`J`.
Next, we construct the Hamiltonian and the solver::
h_int = h_int_density(spin_names, orb_names, map_operator_structure=SK.sumk_to_solver[0], U=Umat, Uprime=Upmat)
S = Solver(beta=beta, gf_struct=gf_struct)
As you see, we take only density-density interactions into
account. Other Hamiltonians with, e.g. with full rotational invariant interactions are:
* h_int_kanamori
* h_int_slater
For other choices of the interaction matrices (e.g Slater representation) or
Hamiltonians, we refer to the reference manual of the :ref:`TRIQS <triqslibs:welcome>`
library.
DMFT cycle
----------
Now we can go to the definition of the self-consistency step. It consists again
of the basic steps discussed in the :ref:`previous section <singleshot>`, with
some additional refinements::
for iteration_number in range(1,loops+1):
if mpi.is_master_node(): print "Iteration = ", iteration_number
SK.symm_deg_gf(S.Sigma_iw,orb=0) # symmetrizing Sigma
SK.set_Sigma([ S.Sigma_iw ]) # put Sigma into the SumK class
chemical_potential = SK.calc_mu( precision = prec_mu ) # find the chemical potential for given density
S.G_iw << SK.extract_G_loc()[0] # calc the local Green function
mpi.report("Total charge of Gloc : %.6f"%S.G_iw.total_density())
# Init the DC term and the real part of Sigma, if no previous runs found:
if (iteration_number==1 and previous_present==False):
dm = S.G_iw.density()
SK.calc_dc(dm, U_interact = U, J_hund = J, orb = 0, use_dc_formula = dc_type)
S.Sigma_iw << SK.dc_imp[0]['up'][0,0]
# Calculate new G0_iw to input into the solver:
S.G0_iw << S.Sigma_iw + inverse(S.G_iw)
S.G0_iw << inverse(S.G0_iw)
# Solve the impurity problem:
S.solve(h_int=h_int, **p)
# Solved. Now do post-solution stuff:
mpi.report("Total charge of impurity problem : %.6f"%S.G_iw.total_density())
# Now mix Sigma and G with factor mix, if wanted:
if (iteration_number>1 or previous_present):
if mpi.is_master_node():
ar = HDFArchive(dft_filename+'.h5','a')
mpi.report("Mixing Sigma and G with factor %s"%mix)
S.Sigma_iw << mix * S.Sigma_iw + (1.0-mix) * ar['dmft_output']['Sigma_iw']
S.G_iw << mix * S.G_iw + (1.0-mix) * ar['dmft_output']['G_iw']
del ar
S.G_iw << mpi.bcast(S.G_iw)
S.Sigma_iw << mpi.bcast(S.Sigma_iw)
# Write the final Sigma and G to the hdf5 archive:
if mpi.is_master_node():
ar = HDFArchive(dft_filename+'.h5','a')
ar['dmft_output']['iterations'] = iteration_number
ar['dmft_output']['G_0'] = S.G0_iw
ar['dmft_output']['G_tau'] = S.G_tau
ar['dmft_output']['G_iw'] = S.G_iw
ar['dmft_output']['Sigma_iw'] = S.Sigma_iw
del ar
# Set the new double counting:
dm = S.G_iw.density() # compute the density matrix of the impurity problem
SK.calc_dc(dm, U_interact = U, J_hund = J, orb = 0, use_dc_formula = dc_type)
# Save stuff into the user_data group of hdf5 archive in case of rerun:
SK.save(['chemical_potential','dc_imp','dc_energ'])
This is all we need for the DFT+DMFT calculation.
You can see in this code snippet, that all results of this calculation
will be stored in a separate subgroup in the hdf5 file, called `dmft_output`.
Note that this script performs 15 DMFT cycles, but does not check for
convergence. Of course, it would be possible to build in convergence criteria.
A simple check for convergence can be also done if you store multiple quantities
of each iteration and analyze the convergence by hand. In general, it is advisable
to start with a lower statistics (less measurements), but then increase it at a
point close to converged results (e.g. after a few initial iterations). This helps
to keep computational costs low during the first iterations.
Using the Kanamori Hamiltonian and the parameters above (but on 16 cores),
your self energy after the **first iteration** should look like the
self energy shown below.
.. image:: images_scripts/SrVO3_Sigma_iw_it1.png
:width: 700
:align: center
.. _tailfit:
Tail fit parameters
-------------------
A good way to identify suitable tail fit parameters is by "human inspection".
Therefore disabled the tail fitting first::
p["perform_tail_fit"] = False
and perform only one DMFT iteration. The resulting self energy can be tail fitted by hand::
for name, sig in S.Sigma_iw:
S.Sigma_iw[name].fit_tail(fit_n_moments = 4, fit_min_n = 60, fit_max_n = 140)
Plot the self energy and adjust the tail fit parameters such that you obtain a
proper fit. The :meth:`fit_tail function <pytriqs.gf.local.tools.tail_fit>` is part
of the :ref:`TRIQS <triqslibs:welcome>` library.
For a self energy which is going to zero for :math:`i\omega \rightarrow 0` our suggestion is
to start the tail fit (:emphasis:`fit_min_n`) at a Matsubara frequency considerable above the minimum
of the self energy and to stop (:emphasis:`fit_max_n`) before the noise fully takes over.
If it is difficult to find a reasonable fit in this region you should increase
your statistics (number of measurements). Keep in mind that :emphasis:`fit_min_n`
and :emphasis:`fit_max_n` also depend on :math:`\beta`.

20
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@ -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 <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.
* :meth:`dos_wannier_basis <dft.sumk_dft_tools.SumkDFTTools.dos_wannier_basis>` for the density of states of the Wannier orbitals and
* :meth:`partial_charges <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)
* :meth:`dos_parproj_basis <dft.sumk_dft_tools.SumkDFTTools.dos_parproj_basis>` for the momentum-integrated spectral function including self energy effects and
* :meth:`spaghettis <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
@ -24,17 +24,17 @@ However, a real frequency self energy has to be provided by the user for the met
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>`::
All tools described below are collected in an extension of the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` class and are
loaded by importing the module :class:`SumkDFTTools <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>`
The initialisation of the class is equivalent to that of the :class:`SumkDFT <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.
Note that all routines available in :class:`SumkDFT <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
@ -110,7 +110,7 @@ real frequency self energy for this purpose. The calculation is done by::
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>`.
in the hdf5 archive. For the structure of `dm`, see also :meth:`reference manual <dft.sumk_dft_tools.SumkDFTTools.partial_charges>`.
Correlated spectral function (with real frequency self energy)
--------------------------------------------------------------
@ -129,7 +129,7 @@ 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>`
option and use the :meth:`convert_bands_input <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_')

115
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@ -34,9 +34,9 @@ some files that we need for the Wannier orbital construction.
The orbital construction itself is done by the Fortran program
:program:`dmftproj`. For an extensive manual to this program see
:download:`TutorialDmftproj.pdf <images_scripts/TutorialDmftproj.pdf>`.
Here we will only describe only the basic steps.
Here we will only describe the basic steps.
Let us take the example of SrVO3, a commonly used
Let us take the compound SrVO3, a commonly used
example for DFT+DMFT calculations. The input file for
:program:`dmftproj` looks like
@ -56,9 +56,9 @@ following 3 to 5 lines:
harmonics).
#. The four numbers refer to *s*, *p*, *d*, and *f* electrons,
resp. Putting 0 means doing nothing, putting 1 will calculate
**unnormalised** projectors in compliance with the Wien2k
**unnormalized** projectors in compliance with the Wien2k
definition. The important flag is 2, this means to include these
electrons as correlated electrons, and calculate normalised Wannier
electrons as correlated electrons, and calculate normalized Wannier
functions for them. In the example above, you see that only for the
vanadium *d* we set the flag to 2. If you want to do simply a DMFT
calculation, then set everything to 0, except one flag 2 for the
@ -100,12 +100,12 @@ directory name):
respectively. These files are needed for projected
density-of-states or spectral-function calculations in
post-processing only.
* :file:`case.oubwin` needed for the charge desity recalculation in
* :file:`case.oubwin` needed for the charge density recalculation in
the case of fully self-consistent DFT+DMFT run (see below).
Now we convert these files into an hdf5 file that can be used for the
DMFT calculations. For this purpose we
use the python module :class:`Wien2kConverter <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter>`. It is initialised as::
use the python module :class:`Wien2kConverter <dft.converters.wien2k_converter.Wien2kConverter>`. It is initialized as::
from pytriqs.applications.dft.converters.wien2k_converter import *
Converter = Wien2kConverter(filename = case)
@ -119,7 +119,7 @@ an hdf5 archive, named :file:`case.h5`, where all the data is
stored. For other parameters of the constructor please visit the
:ref:`refconverters` section of the reference manual.
After initialising the interface module, we can now convert the input
After initializing the interface module, we can now convert the input
text files to the hdf5 archive by::
Converter.convert_dft_input()
@ -133,18 +133,18 @@ 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 <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.dos_wannier_basis>`
contained in the module :class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>` to check the density of
At this point you should use the method :meth:`dos_wannier_basis <dft.sumk_dft_tools.SumkDFTTools.dos_wannier_basis>`
contained in the module :class:`SumkDFTTools <dft.sumk_dft_tools.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`.
proceed with the section on :ref:`single-shot DFT+DMFT calculations <singleshot>`.
Data for post-processing
""""""""""""""""""""""""
In case you want to do post-processing of your data using the module
:class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>`, some more files
:class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>`, some more files
have to be converted to the hdf5 archive. For instance, for
calculating the partial density of states or partial charges
consistent with the definition of :program:`Wien2k`, you have to invoke::
@ -165,7 +165,7 @@ following. First, one has to do the Wien2k calculation on the given
Again, maybe with the optional additional extra flags according to
Wien2k. Now we use a routine of the converter module allows to read
and convert the input for :class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>`::
and convert the input for :class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>`::
Converter.convert_bands_input()
@ -255,10 +255,10 @@ A general H(k)
--------------
In addition to the more complicated Wien2k converter,
:program:`dft_tools` contains also a light converter. It takes only
:program:`DFTTools` contains also a light converter. It takes only
one inputfile, and creates the necessary hdf outputfile for
the DMFT calculation. The header of this input file has to have the
following format:
the DMFT calculation. The header of this input file has a defined
format, an example is the following:
.. literalinclude:: images_scripts/case.hk
@ -266,22 +266,74 @@ The lines of this header define
#. Number of :math:`\mathbf{k}`-points used in the calculation
#. Electron density for setting the chemical potential
#. Number of correlated atoms in the unit cell
#. The next line contains four numbers: index of the atom, index
of the correlated shell, :math:`l` quantum number, dimension
of this shell. Repeat this line for each correlated atom.
#. Number of total atomic shells in the hamiltonian matrix. In short,
this gives the number of lines described in the following. IN the
example file give above this number is 2.
#. The next line(s) contain four numbers each: index of the atom, index
of the equivalent shell, :math:`l` quantum number, dimension
of this shell. Repeat this line for each atomic shell, the number
of the shells is given in the previous line.
In the example input file given above, we have two inequivalent
atomic shells, one on atom number 1 with a full d-shell (dimension 5),
and one on atom number 2 with one p-shell (dimension 3).
Other examples for these lines are:
#. Full d-shell in a material with only one correlated atom in the
unit cell (e.g. SrVO3). One line is sufficient and the numbers
are `1 1 2 5`.
#. Full d-shell in a material with two equivalent atoms in the unit
cell (e.g. FeSe): You need two lines, one for each equivalent
atom. First line is `1 1 2 5`, and the second line is
`2 1 2 5`. The only difference is the first number, which tells on
which atom the shell is located. The second number is the
same in both lines, meaning that both atoms are equivalent.
#. t2g orbitals on two non-equivalent atoms in the unit cell: Two
lines again. First line is `1 1 2 3`, second line `2 2 2 3`. The
difference to the case above is that now also the second number
differs. Therefore, the two shells are treated independently in
the calculation.
#. d-p Hamiltonian in a system with two equivalent atoms each in
the unit cell (e.g. FeSe has two Fe and two Se in the unit
cell). You need for lines. First line `1 1 2 5`, second
line
`2 1 2 5`. These two lines specify Fe as in the case above. For the p
orbitals you need line three as `3 2 1 3` and line four
as `4 2 1 3`. We have 4 atoms, since the first number runs from 1 to 4,
but only two inequivalent atoms, since the second number runs
only form 1 to 2.
Note that the total dimension of the hamiltonian matrices that are
read in is the sum of all shell dimensions that you specified. For
example number 4 given above we have a dimension of 5+5+3+3=16. It is important
that the order of the shells that you give here must be the same as
the order of the orbitals in the hamiltonian matrix. In the last
example case above the code assumes that matrix index 1 to 5
belongs to the first d shell, 6 to 10 to the second, 11 to 13 to
the first p shell, and 14 to 16 the second p shell.
#. Number of correlated shells in the hamiltonian matrix, in the same
spirit as line 3.
#. The next line(s) contain six numbers: index of the atom, index
of the equivalent shell, :math:`l` quantum number, dimension
of the correlated shells, a spin-orbit parameter, and another
parameter defining interactions. Note that the latter two
parameters are not used at the moment in the code, and only kept
for compatibility reasons. In our example file we use only the
d-shell as correlated, that is why we have only one line here.
#. The last line contains several numbers: the number of irreducible
representations, and then the dimensions of the irreps. One
possibility is as the example above, another one would be 2
2 3. Thiw would mean, 2 irreps (eg and t2g), of dimension 2 and 3,
2 3. This would mean, 2 irreps (eg and t2g), of dimension 2 and 3,
resp.
After these header lines, the file has to contain the Hamiltonian
matrix in orbital space. The standard convention is that you give for
each
:math:`\mathbf{k}`-point first the matrix of the real part, then the
matrix of the imaginary part, and then move on to the next
:math:`\mathbf{k}`-point.
each :math:`\mathbf{k}`-point first the matrix of the real part, then the
matrix of the imaginary part, and then move on to the next :math:`\mathbf{k}`-point.
The converter itself is used as::
@ -290,8 +342,7 @@ The converter itself is used as::
Converter.convert_dft_input()
where :file:`hkinputfile` is the name of the input file described
above. This produces the hdf file that you need, and you cna proceed
with the
above. This produces the hdf file that you need for a DMFT calculation.
For more options of this converter, have a look at the
:ref:`refconverters` section of the reference manual.
@ -301,10 +352,10 @@ Wannier90 Converter
-------------------
Using this converter it is possible to convert the output of
:program:`Wannier90` (http://wannier.org) calculations of
`wannier90 <http://wannier.org>`_
Maximally Localized Wannier Functions (MLWF) and create a HDF5 archive
suitable for one-shot DMFT calculations with the
:class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` class.
:class:`SumkDFT <dft.sumk_dft.SumkDFT>` class.
The user must supply two files in order to run the Wannier90 Converter:
@ -375,7 +426,7 @@ In our `Pnma`-LaVO\ :sub:`3` example, for instance, we could use::
where the ``x=-1,1,0`` option indicates that the V--O bonds in the octahedra are
rotated by (approximatively) 45 degrees with respect to the axes of the `Pbnm` cell.
The converter will analyse the matrix elements of the local hamiltonian
The converter will analyze the matrix elements of the local Hamiltonian
to find the symmetry matrices `rot_mat` needed for the global-to-local
transformation of the basis set for correlated orbitals
(see section :ref:`hdfstructure`).
@ -400,7 +451,7 @@ The current implementation of the Wannier90 Converter has some limitations:
* Calculations with spin-orbit (``SO=1``) are not supported.
* The spin-polarized case (``SP=1``) is not yet tested.
* The post-processing routines in the module
:class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>`
:class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>`
were not tested with this converter.
* ``proj_mat_all`` are not used, so there are no projectors onto the
uncorrelated orbitals for now.
@ -413,8 +464,8 @@ The interface packages are written such that all the file operations
are done only on the master node. In general, the philosophy of the
package is that whenever you read in something from the archive
yourself, you have to *manually* broadcast it to the nodes. An
exception to this rule is when you use routines from :class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>`
or :class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>`, where the broadcasting is done for you.
exception to this rule is when you use routines from :class:`SumkDFT <dft.sumk_dft.SumkDFT>`
or :class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>`, where the broadcasting is done for you.
Interfaces to other packages
----------------------------

2
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@ -21,7 +21,7 @@ Wien2k + dmftproj
:ref:`conversion`, or the extensive :download:`dmftproj manual<images_scripts/TutorialDmftproj.pdf>`.
In the following, we discuss how to use the
:ref:`TRIQS <triqslibs:welcome>` tools in combination with the :program:`Wien2k` program.
:ref:`TRIQS <triqslibs:install>` tools in combination with the :program:`Wien2k` program.
We can use the DMFT script as introduced in section :ref:`singleshot`,
with just a few simple

256
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@ -5,16 +5,21 @@
Single-shot DFT+DMFT
====================
After having set up the hdf5 archive, we can now proceed to our first DFT+DMFT calculation.
It consists of initialization steps, and the actual DMFT self-consistency loop,
With the code snippets below you can build your own script and target
it to your needs. Little examples on :ref:`mixing <mixing>` and on
:ref:`restarting from a previous calculation <restartcalc>` at the end of this page
should also demonstrate how simple you can modify your own DMFT script. A full working
calculation for SrVO3 is discussed in the :ref:`next section <SrVO3>`.
After having set up the hdf5 archive, we can now do our DFT+DMFT calculation. It consists of
initialization steps, and the actual DMFT self-consistency loop, as is
discussed below.
Initialisation of the calculation
Initialization of the calculation
---------------------------------
Before doing the calculation, we have to intialize all the objects that we will need. The first thing is the
:class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` class. It contains all basic routines that are necessary to perform a summation in k-space
Before doing the actual calculation, we have to initialize all needed objects.
The first thing is the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` class.
It contains all basic routines that are necessary to perform a summation in k-space
to get the local quantities used in DMFT. It is initialized by::
from pytriqs.applications.dft.sumk_dft import *
@ -25,35 +30,34 @@ Setting up the impurity solver
------------------------------
The next step is to setup an impurity solver. There are different
solvers available within the :ref:`TRIQS <triqslibs:welcome>` framework. Below, we will discuss
the example of the hybridisation
solvers available within the :ref:`TRIQS <triqslibs:welcome>` framework.
E.g. for :ref:`SrVO3 <SrVO3>`, we will use the hybridization
expansion :ref:`CTHYB solver <triqscthyb:welcome>`. Later on, we will
see also the example of the Hubbard-I solver. They all have in common,
that they are called by a uniform command::
see also the example of the `Hubbard-I solver <https://triqs.ipht.cnrs.fr/1.x/applications/hubbardI/>`_.
They all have in common, that they are called by an uniform command::
S.solve(params)
where `params` are the solver parameters and depend on the actual
solver that is used. Before going into the details of the solver, let
us discuss in the next section how to perform the DMFT loop using
the methods of :program:`dft_tools`, assuming that we have set up a
working solver instance.
where :emphasis:`params` are the solver parameters and depend on the actual
solver. Setting up the :ref:`CTHYB solver <triqscthyb:welcome>` for SrVO3 is
discussed on the :ref:`next page <SrVO3>`. Here, let us now perform the DMFT
loop using the methods of :program:`DFTTools`, assuming that we have already
set up a working solver instance.
Doing the DMFT loop
-------------------
Having initialized the SumK class and the Solver, we can proceed with the DMFT
loop itself. We have to set up the loop over DMFT
iterations and the self-consistency condition::
Having initialized the :class:`Sumk class <dft.sumk_dft.SumkDFT>`
and the solver, we can proceed with the actual DMFT part of the calculation.
We set up the loop over DMFT iterations and the self-consistency condition::
n_loops = 5
n_loops = 15
for iteration_number in range(n_loops) : # start the DMFT loop
SK.set_Sigma([ S.Sigma ]) # Put self energy to the SumK class
chemical_potential = SK.calc_mu() # calculate the chemical potential for the given density
S.G_iw << SK.extract_G_loc()[0] # extract the local Green function
S.G0_iw << inverse(S.Sigma_iw + inverse(S.G_iw)) # finally get G0, the input for the Solver
S.G0_iw << inverse(S.Sigma_iw + inverse(S.G_iw)) # finally get G0, the input for the solver
S.solve(h_int=h_int, **p) # now solve the impurity problem
@ -61,24 +65,18 @@ iterations and the self-consistency condition::
SK.calc_dc(dm, U_interact=U, J_hund=J, orb=0, use_dc_formula=1) # Set the double counting term
SK.save(['chemical_potential','dc_imp','dc_energ']) # Save data in the hdf5 archive
These basic steps are enough to set up the basic DMFT Loop. For a detailed
description of the :class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` routines, see the reference
manual.
After
the self-consistency steps (extracting a new :math:`G^0(i\omega)`),
the Anderson impurity problem is solved.
Different to model calculations, we have to do a few
These steps are enough for a basic DMFT Loop.
After the self-consistency steps, which lead to a new :math:`G^0(i\omega)`,
the impurity solver is called. Different to model calculations, we have to do a few
more steps after this, because of the double-counting correction. We first
calculate the density of the impurity problem. Then, the routine `calc_dc`
calculate the density of the impurity problem. Then, the routine :meth:`calc_dc <dft.sumk_dft.SumkDFT.calc_dc>`
takes as parameters this density matrix, the Coulomb interaction, Hund's rule
coupling, and the type of double-counting that should be used. Possible values
for `use_dc_formula` are:
for :emphasis:`use_dc_formula` are:
* `0`: Full-localised limit
* `0`: Full-localised limit (FLL)
* `1`: DC formula as given in K. Held, Adv. Phys. 56, 829 (2007).
* `2`: Around-mean-field
* `2`: Around-mean-field (AMF)
At the end of the calculation, we can save the Greens function and self energy into a file::
@ -89,65 +87,21 @@ At the end of the calculation, we can save the Greens function and self energy i
ar["G"] = S.G_iw
ar["Sigma"] = S.Sigma_iw
This is it!
These are the essential steps necessary for a one-shot DFT+DMFT calculation.
For a detailed description of the :class:`SumkDFT <dft.sumk_dft.SumkDFT>`
routines, see the :ref:`reference manual <reference>`. To perform full charge self-consistent calculations, there
are some more things to consider, which we will see :ref:`later on <full_charge_selfcons>`.
These are the essential steps to do a one-shot DFT+DMFT calculation.
For full charge-self consistent calculations, there are some more things
to consider, which we will see later on.
.. _restartcalc:
A full DFT+DMFT calculation
---------------------------
Restarting a calculation
------------------------
We will discuss now how to set up a full working calculation,
including setting up the CTHYB solver, and specifying some more parameters
in order to make the calculation more efficient. Here, we
will see a more advanced example, which is also suited for parallel
execution. For the convenience of the user, we provide also two
working python scripts in this documentation. One for a calculation
using Kanamori definitions (:download:`dft_dmft_cthyb.py
<images_scripts/dft_dmft_cthyb.py>`) and one with a
rotational-invariant Slater interaction Hamiltonian (:download:`dft_dmft_cthyb_slater.py
<images_scripts/dft_dmft_cthyb.py>`). The user has to adapt these
scripts to his own needs.
First, we load the necessary modules::
from pytriqs.applications.dft.sumk_dft import *
from pytriqs.gf.local import *
from pytriqs.archive import HDFArchive
from pytriqs.operators.util import *
from pytriqs.applications.impurity_solvers.cthyb import *
The last two lines load the modules for the construction of the CTHYB
solver.
Then we define some parameters::
dft_filename='SrVO3'
U = 4.0
J = 0.65
beta = 40
loops = 10 # Number of DMFT sc-loops
sigma_mix = 0.8 # Mixing factor of Sigma after solution of the AIM
dc_type = 1 # DC type: 0 FLL, 1 Held, 2 AMF
use_blocks = True # use bloc structure from DFT input
prec_mu = 0.0001
# Solver parameters
p = {}
p["length_cycle"] = 200
p["n_warmup_cycles"] = 2000
p["n_cycles"] = 20000
Most of these parameters are self-explanatory. The first,
`dft_filename`, gives the filename of the input files. For more
details on the solver parameters, we refer the user to
the :ref:`CTHYB solver <triqscthyb:welcome>` documentation.
We assume that the conversion to the hdf5 archive is already done. We
can check now in this archive, if previous runs are present, or if we have to start
from scratch::
Often only a few DMFT iterations are performed first, and thus, it is desirable to
carry out further iterations, e.g. to improve on the convergence. With a little modification
at the initialization stage (before the DMFT loop) it is possible to detect if previous runs
are present, or if the calculation should start from scratch::
previous_runs = 0
previous_present = False
@ -165,127 +119,49 @@ from scratch::
previous_present = mpi.bcast(previous_present)
You can see in this code snippet, that all results of this calculation
will be stored in a separate subgroup in the hdf5 file, called
`dmft_output`. Removing this subgroup allows you to reset your
calculation to the starting point easily.
Now we can use all this information to initialise the :class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` class::
SK = SumkDFT(hdf_file=dft_filename+'.h5',use_dft_blocks=use_blocks)
The next step is to initialise the :class:`Solver <pytriqs.applications.impurity_solvers.cthyb.Solver>` class. It consist
of two steps
#. Calculating the multi-band interaction matrix, and setting up the
interaction Hamiltonian
#. Setting up the solver class
The first step is done using methods of
the :ref:`TRIQS <triqslibs:welcome>` library::
n_orb = SK.corr_shells[0]['dim']
l = SK.corr_shells[0]['l']
spin_names = ["up","down"]
orb_names = [i for i in range(n_orb)]
# Use GF structure determined by DFT blocks:
gf_struct = SK.gf_struct_solver[0]
# Construct U matrix for density-density calculations:
Umat, Upmat = U_matrix_kanamori(n_orb=n_orb, U_int=U, J_hund=J)
We assumed here that we want to use an interaction matrix with
Kanamori definitions of :math:`U` and :math:`J`. For
other choices (Slater interaction matrix for instance), and other
parameters, we refer to the reference manual
of the :ref:`TRIQS <triqslibs:welcome>` library.
Next, we construct the Hamiltonian and the solver::
h_int = h_int_density(spin_names, orb_names, map_operator_structure=SK.sumk_to_solver[0], U=Umat, Uprime=Upmat)
S = Solver(beta=beta, gf_struct=gf_struct)
As you see, we take only density-density interactions into
account. Other choices for the Hamiltonian are
* h_int_kanamori
* h_int_slater
These two include full rotational invariant interactions. Again,
options can be found in the :ref:`TRIQS <triqslibs:welcome>` library
reference manual.
If there are previous runs stored in the hdf5 archive, we can now load the self energy
of the last iteration::
You can see from this code snippet, that removing the subgroup :emphasis:`dmft_results` from the
hdf file has the effect of reseting the calculation to the starting point. If there are previous
runs stored in the hdf5 archive, we can now load the self energy, the chemical potential and
double counting values of the last iteration::
if previous_present:
if mpi.is_master_node():
ar = HDFArchive(dft_filename+'.h5','a')
S.Sigma_iw << ar['dmft_output']['Sigma_iw']
del ar
chemical_potential,dc_imp,dc_energ = SK.load(['chemical_potential','dc_imp','dc_energ'])
S.Sigma_iw << mpi.bcast(S.Sigma_iw)
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)
The self-energy is broadcast from the master node to the slave nodes. Also, the
last saved chemical potential and double counting values are read in and set.
The data is loaded only on the master node, and therefore we broadcast it to the slave nodes.
Be careful when storing the :emphasis:`iteration_number` as we also have to add the previous
iteration count::
Now we can go to the definition of the self-consistency step. It consists again
of the basic steps discussed in the previous section, with some additional
refinements::
ar['dmft_output']['iterations'] = iteration_number + previous_runs
for iteration_number in range(1,loops+1):
if mpi.is_master_node(): print "Iteration = ", iteration_number
.. _mixing:
SK.symm_deg_gf(S.Sigma_iw,orb=0) # symmetrise Sigma
SK.set_Sigma([ S.Sigma_iw ]) # put Sigma into the SumK class
chemical_potential = SK.calc_mu( precision = prec_mu ) # find the chemical potential for given density
S.G_iw << SK.extract_G_loc()[0] # calc the local Green function
mpi.report("Total charge of Gloc : %.6f"%S.G_iw.total_density())
# Init the DC term and the real part of Sigma, if no previous runs found:
if (iteration_number==1 and previous_present==False):
dm = S.G_iw.density()
SK.calc_dc(dm, U_interact = U, J_hund = J, orb = 0, use_dc_formula = dc_type)
S.Sigma_iw << SK.dc_imp[0]['up'][0,0]
Mixing
------
# Calculate new G0_iw to input into the solver:
S.G0_iw << S.Sigma_iw + inverse(S.G_iw)
S.G0_iw << inverse(S.G0_iw)
In some cases a mixing of two consecutive self energies (or alternatively two hybridization
functions) can be necessary in order to ensure convergence::
# Solve the impurity problem:
S.solve(h_int=h_int, **p)
# Solved. Now do post-solution stuff:
mpi.report("Total charge of impurity problem : %.6f"%S.G_iw.total_density())
# Now mix Sigma and G with factor sigma_mix, if wanted:
mix = 0.8 # mixing factor
if (iteration_number>1 or previous_present):
if mpi.is_master_node():
ar = HDFArchive(dft_filename+'.h5','a')
mpi.report("Mixing Sigma and G with factor %s"%sigma_mix)
S.Sigma_iw << sigma_mix * S.Sigma_iw + (1.0-sigma_mix) * ar['dmft_output']['Sigma_iw']
S.G_iw << sigma_mix * S.G_iw + (1.0-sigma_mix) * ar['dmft_output']['G_iw']
mpi.report("Mixing Sigma and G with factor %s"%mix)
S.Sigma_iw << mix * S.Sigma_iw + (1.0-mix) * ar['dmft_output']['Sigma_iw']
S.G_iw << mix * S.G_iw + (1.0-mix) * ar['dmft_output']['G_iw']
del ar
S.G_iw << mpi.bcast(S.G_iw)
S.Sigma_iw << mpi.bcast(S.Sigma_iw)
# Write the final Sigma and G to the hdf5 archive:
if mpi.is_master_node():
ar = HDFArchive(dft_filename+'.h5','a')
ar['dmft_output']['iterations'] = iteration_number + previous_runs
ar['dmft_output']['G_0'] = S.G0_iw
ar['dmft_output']['G_tau'] = S.G_tau
ar['dmft_output']['G_iw'] = S.G_iw
ar['dmft_output']['Sigma_iw'] = S.Sigma_iw
del ar
# Set the new double counting:
dm = S.G_iw.density() # compute the density matrix of the impurity problem
SK.calc_dc(dm, U_interact = U, J_hund = J, orb = 0, use_dc_formula = dc_type)
# Save stuff into the dft_output group of hdf5 archive in case of rerun:
SK.save(['chemical_potential','dc_imp','dc_energ'])
This is all we need for the DFT+DMFT calculation. At the end, all results are stored in the hdf5 output file.
In this little piece of code, which should be placed after calling the solver, two consecutive
self energies are linearly mixed with the factor :emphasis:`mix`. Of course, it is possible
to implement more advanced mixing schemes (e.g. Broyden's methods), however, in most cases
simple linear mixing or even no mixing is sufficient for a reasonably fast convergence.

4
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@ -89,7 +89,7 @@ however there are also some differences. First difference is that we import the
The Hubbard-I solver is very fast and we do not need to take into account the DFT block structure or use any approximation for the *U*-matrix.
We load and convert the :program:`dmftproj` output and initialize the
:class:`SumkDFT <pytriqs.applications.dft.sumk_dft.SumkDFT>` class as described in :ref:`conversion` and
:class:`SumkDFT <dft.sumk_dft.SumkDFT>` class as described in :ref:`conversion` and
:ref:`singleshot` and then set up the Hubbard-I solver ::
S = Solver(beta = beta, l = l)
@ -206,7 +206,7 @@ symmetries::
Converter.convert_parpoj_input()
To get access to analysing tools we initialize the
:class:`SumkDFTTools <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools>` class ::
:class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>` class ::
SK = SumkDFTTools(hdf_file=dft_filename+'.h5', use_dft_blocks=False)

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@ -1,5 +1,8 @@
64 ! number of k-points
1.0 ! Electron density
1 ! number of correlated atoms
2 ! number of total atomic shells
1 1 2 5 ! iatom, isort, l, dimension
2 2 1 3 ! iatom, isort, l, dimension
1 ! number of correlated shells
1 1 2 5 0 0 ! iatom, isort, l, dimension, SO, irep
1 5 ! # of ireps, dimension of irep

18
doc/guide/images_scripts/dft_dmft_cthyb.py
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@ -6,10 +6,10 @@ from pytriqs.gf.local import *
from pytriqs.applications.dft.sumk_dft import *
dft_filename='SrVO3'
U = U.0
U = 4.0
J = 0.65
beta = 40
loops = 10 # Number of DMFT sc-loops
loops = 15 # Number of DMFT sc-loops
sigma_mix = 1.0 # Mixing factor of Sigma after solution of the AIM
delta_mix = 1.0 # Mixing factor of Delta as input for the AIM
dc_type = 1 # DC type: 0 FLL, 1 Held, 2 AMF
@ -20,9 +20,14 @@ h_field = 0.0
# Solver parameters
p = {}
p["max_time"] = -1
p["length_cycle"] = 50
p["n_warmup_cycles"] = 50
p["n_cycles"] = 5000
p["random_seed"] = 123 * mpi.rank + 567
p["length_cycle"] = 200
p["n_warmup_cycles"] = 100000
p["n_cycles"] = 1000000
p["perfrom_tail_fit"] = True
p["fit_max_moments"] = 4
p["fit_min_n"] = 30
p["fit_max_n"] = 60
# If conversion step was not done, we could do it here. Uncomment the lines it you want to do this.
#from pytriqs.applications.dft.converters.wien2k_converter import *
@ -141,6 +146,5 @@ for iteration_number in range(1,loops+1):
dm = S.G_iw.density() # compute the density matrix of the impurity problem
SK.calc_dc(dm, U_interact = U, J_hund = J, orb = 0, use_dc_formula = dc_type)
# Save stuff into the dft_output group of hdf5 archive in case of rerun:
# Save stuff into the user_data group of hdf5 archive in case of rerun:
SK.save(['chemical_potential','dc_imp','dc_energ'])

15
doc/guide/images_scripts/dft_dmft_cthyb_slater.py
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@ -6,7 +6,7 @@ from pytriqs.gf.local import *
from pytriqs.applications.dft.sumk_dft import *
from pytriqs.applications.dft.converters.wien2k_converter import *
dft_filename='Gd_fcc'
dft_filename='SrVO3'
U = 9.6
J = 0.8
beta = 40
@ -21,9 +21,14 @@ h_field = 0.0
# Solver parameters
p = {}
p["max_time"] = -1
p["length_cycle"] = 50
p["n_warmup_cycles"] = 50
p["n_cycles"] = 5000
p["random_seed"] = 123 * mpi.rank + 567
p["length_cycle"] = 200
p["n_warmup_cycles"] = 100000
p["n_cycles"] = 1000000
p["perfrom_tail_fit"] = True
p["fit_max_moments"] = 4
p["fit_min_n"] = 30
p["fit_max_n"] = 60
# If conversion step was not done, we could do it here. Uncomment the lines it you want to do this.
#from pytriqs.applications.dft.converters.wien2k_converter import *
@ -144,5 +149,3 @@ for iteration_number in range(1,loops+1):
# Save stuff into the dft_output group of hdf5 archive in case of rerun:
SK.save(['chemical_potential','dc_imp','dc_energ'])

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@ -1,7 +1,7 @@
.. _Transport:
Transport calculations test
======================
Transport calculations
============================
Formalism
---------
@ -44,13 +44,13 @@ real-frequency self energy by doing an analytic continuation.
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:
Besides the self energy the Wien2k files read by the transport converter (:meth:`convert_transport_input <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.
* :file:`.outputs`: In this file the k-point symmetries are given.
* :file:`.oubwin`: Contains the indices of the bands within the projected subspace (written by :program:`dmftproj`) for each k-point.
* :file:`.pmat`: This file is the output of the Wien2k optics package and contains the velocity (momentum) matrix elements between all bands in the desired energy
window for each k-point. How to use the optics package is described below.
* :file:`.h5`: The hdf5 archive has to be present and should contain the dft_input subgroup. Otherwise :meth:`convert_dft_input <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter.convert_dft_input>` needs to be called before :meth:`convert_transport_input <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>`.
* :file:`.h5`: The hdf5 archive has to be present and should contain the dft_input subgroup. Otherwise :meth:`convert_dft_input <dft.converters.wien2k_converter.Wien2kConverter.convert_dft_input>` needs to be called before :meth:`convert_transport_input <dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>`.
Wien2k optics package
@ -84,7 +84,7 @@ 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>`
The converter :meth:`convert_transport_input <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::
@ -104,7 +104,7 @@ Here the transport distribution is calculated in :math:`xx` direction for the fr
To use the previously obtained self energy we set with_Sigma to True and the broadening to :math:`0.0`.
As we also want to calculate the Seebeck coefficient we have to include :math:`\Omega=0.0` in the mesh.
Note that the current version of the code repines the :math:`\Omega` values to the closest values on the self energy mesh.
For complete description of the input parameters see the :meth:`transport_distribution reference <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`.
For complete description of the input parameters see the :meth:`transport_distribution reference <dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`.
The resulting transport distribution is not automatically saved, but this can be easily achieved with::

8
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@ -1,11 +1,11 @@
.. index:: DFT Tools
.. index:: DFTTools
.. module:: pytriqs.applications.dft
.. _dfttools:
.. _dft:
DFT Tools
=========
DFTTools
========
This :ref:`TRIQS-based <triqslibs:welcome>`-based application is aimed
at ab-initio calculations for

22
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@ -0,0 +1,22 @@
Block Structure
===============
The `BlockStructure` class allows to change and manipulate
Green's functions structures and mappings from sumk to solver.
The block structure can also be written to and read from HDF files.
.. warning::
Do not write the individual elements of this class to a HDF file,
as they belong together and changing one without the other can
result in unexpected results. Always write the BlockStructure
object as a whole.
Writing the sumk_to_solver and solver_to_sumk elements
individually is not implemented.
.. autoclass:: dft.block_structure.BlockStructure
:members:
:show-inheritance:

2
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@ -17,7 +17,7 @@ H(k) Converter
:special-members:
Wannier90 Converter
--------------
-------------------
.. autoclass:: dft.converters.wannier90_converter.Wannier90Converter
:members:
:special-members:

2
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@ -2,7 +2,7 @@ SumK DFT
========
.. autoclass:: sumk_dft.SumkDFT
.. autoclass:: dft.sumk_dft.SumkDFT
:members:
:special-members:
:show-inheritance:

2
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@ -2,7 +2,7 @@ SumK DFT Tools
==============
.. autoclass:: sumk_dft_tools.SumkDFTTools
.. autoclass:: dft.sumk_dft_tools.SumkDFTTools
:members:
:special-members:
:show-inheritance:

2
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@ -1,6 +1,6 @@
Symmetry
========
.. autoclass:: Symmetry
.. autoclass:: dft.Symmetry
:members:
:special-members:

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@ -1,6 +1,6 @@
TransBasis
==========
.. autoclass:: trans_basis.TransBasis
.. autoclass:: dft.trans_basis.TransBasis
:members:
:special-members:

5
python/CMakeLists.txt
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@ -8,4 +8,9 @@ configure_file(${CMAKE_SOURCE_DIR}/cmake/sitecustomize.py ${CMAKE_CURRENT_BINARY
# make a local pytriqs copy
triqs_prepare_local_pytriqs(${python_destination})
# VASP converter
add_subdirectory(converters/plovasp)
# add version file
configure_file(version.py.in version.py)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${TRIQS_PYTHON_LIB_DEST_ROOT}/${python_destination})

8
python/__init__.py
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@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,11 +18,13 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
from sumk_dft import SumkDFT
from symmetry import Symmetry
from block_structure import BlockStructure
from sumk_dft_tools import SumkDFTTools
from converters import *
__all__=['SumkDFT','Symmetry','SumkDFTTools','Wien2kConverter','HkConverter']
__all__ = ['SumkDFT', 'Symmetry', 'SumkDFTTools',
'Wien2kConverter', 'HkConverter','BlockStructure']

442
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@ -0,0 +1,442 @@
import copy
import numpy as np
from pytriqs.gf.local import GfImFreq, BlockGf
from ast import literal_eval
from warnings import warn
class BlockStructure(object):
""" Contains information about the Green function structure.
This class contains information about the structure of the solver
and sumk Green functions and the mapping between them.
Parameters
----------
gf_struct_sumk : list of list of tuple
gf_struct_sumk[ish][idx] = (block_name,list of indices in block)
for correlated shell ish; idx is just a counter in the list
gf_struct_solver : list of dict
gf_struct_solver[ish][block] = list of indices in that block
for *inequivalent* correlated shell ish
solver_to_sumk : list of dict
solver_to_sumk[ish][(from_block,from_idx)] = (to_block,to_idx)
maps from the solver block and index to the sumk block and index
for *inequivalent* correlated shell ish
sumk_to_solver : list of dict
sumk_to_solver[ish][(from_block,from_idx)] = (to_block,to_idx)
maps from the sumk block and index to the solver block and index
for *inequivalent* correlated shell ish
solver_to_sumk_block : list of dict
solver_to_sumk_block[ish][from_block] = to_block
maps from the solver block to the sumk block
for *inequivalent* correlated shell ish
"""
def __init__(self,gf_struct_sumk=None,
gf_struct_solver=None,
solver_to_sumk=None,
sumk_to_solver=None,
solver_to_sumk_block=None):
self.gf_struct_sumk = gf_struct_sumk
self.gf_struct_solver = gf_struct_solver
self.solver_to_sumk = solver_to_sumk
self.sumk_to_solver = sumk_to_solver
self.solver_to_sumk_block = solver_to_sumk_block
@classmethod
def full_structure(cls,gf_struct,corr_to_inequiv):
""" Construct structure that maps to itself.
This has the same structure for sumk and solver, and the
mapping solver_to_sumk and sumk_to_solver is one-to-one.
Parameters
----------
gf_struct : list of dict
gf_struct[ish][block] = list of indices in that block
for (inequivalent) correlated shell ish
corr_to_inequiv : list
gives the mapping from correlated shell csh to inequivalent
correlated shell icsh, so that corr_to_inequiv[csh]=icsh
e.g. SumkDFT.corr_to_inequiv
if None, each inequivalent correlated shell is supposed to
be correspond to just one correlated shell with the same
index; there is not default, None has to be set explicitly!
"""
solver_to_sumk = []
s2sblock = []
gs_sumk = []
for ish in range(len(gf_struct)):
so2su = {}
so2sublock = {}
gss = []
for block in gf_struct[ish]:
so2sublock[block]=block
for ind in gf_struct[ish][block]:
so2su[(block,ind)]=(block,ind)
gss.append((block,gf_struct[ish][block]))
solver_to_sumk.append(so2su)
s2sblock.append(so2sublock)
gs_sumk.append(gss)
# gf_struct_sumk is not given for each inequivalent correlated
# shell, but for every correlated shell!
if corr_to_inequiv is not None:
gs_sumk_all = [None]*len(corr_to_inequiv)
for i in range(len(corr_to_inequiv)):
gs_sumk_all[i] = gs_sumk[corr_to_inequiv[i]]
else:
gs_sumk_all = gs_sumk
return cls(gf_struct_solver=copy.deepcopy(gf_struct),
gf_struct_sumk = gs_sumk_all,
solver_to_sumk = copy.deepcopy(solver_to_sumk),
sumk_to_solver = solver_to_sumk,
solver_to_sumk_block = s2sblock)
def pick_gf_struct_solver(self,new_gf_struct):
""" Pick selected orbitals within blocks.
This throws away parts of the Green's function that (for some
reason - be sure that you know what you're doing) shouldn't be
included in the calculation.
To drop an entire block, just don't include it.
To drop a certain index within a block, just don't include it.
If it was before:
[{'up':[0,1],'down':[0,1],'left':[0,1]}]
to choose the 0th index of the up block and the 1st index of
the down block and drop the left block, the new_gf_struct would
have to be
[{'up':[0],'down':[1]}]
Note that the indices will be renamed to be a 0-based
sequence of integers, i.e. the new structure will actually
be [{'up':[0],'down':[0]}].
For dropped indices, sumk_to_solver will map to (None,None).
Parameters
----------
new_gf_struct : list of dict
formatted the same as gf_struct_solver:
new_gf_struct[ish][block]=list of indices in that block.
"""
for ish in range(len(self.gf_struct_solver)):
gf_struct = new_gf_struct[ish]
# create new solver_to_sumk
so2su={}
so2su_block = {}
for blk,idxs in gf_struct.items():
for i in range(len(idxs)):
so2su[(blk,i)]=self.solver_to_sumk[ish][(blk,idxs[i])]
so2su_block[blk]=so2su[(blk,i)][0]
self.solver_to_sumk[ish] = so2su
self.solver_to_sumk_block[ish] = so2su_block
# create new sumk_to_solver
for k,v in self.sumk_to_solver[ish].items():
blk,ind=v
if blk in gf_struct and ind in gf_struct[blk]:
new_ind = gf_struct[blk].index(ind)
self.sumk_to_solver[ish][k]=(blk,new_ind)
else:
self.sumk_to_solver[ish][k]=(None,None)
# reindexing gf_struct so that it starts with 0
for k in gf_struct:
gf_struct[k]=range(len(gf_struct[k]))
self.gf_struct_solver[ish]=gf_struct
def pick_gf_struct_sumk(self,new_gf_struct):
""" Pick selected orbitals within blocks.
This throws away parts of the Green's function that (for some
reason - be sure that you know what you're doing) shouldn't be
included in the calculation.
To drop an entire block, just don't include it.
To drop a certain index within a block, just don't include it.
If it was before:
[{'up':[0,1],'down':[0,1],'left':[0,1]}]
to choose the 0th index of the up block and the 1st index of
the down block and drop the left block, the new_gf_struct would
have to be
[{'up':[0],'down':[1]}]
Note that the indices will be renamed to be a 0-based
sequence of integers.
For dropped indices, sumk_to_solver will map to (None,None).
Parameters
----------
new_gf_struct : list of dict
formatted the same as gf_struct_solver:
new_gf_struct[ish][block]=list of indices in that block.
However, the indices are not according to the solver Gf
but the sumk Gf.
"""
gfs = []
# construct gfs, which is the equivalent of new_gf_struct
# but according to the solver Gf, by using the sumk_to_solver
# mapping
for ish in range(len(new_gf_struct)):
gfs.append({})
for block in new_gf_struct[ish].keys():
for ind in new_gf_struct[ish][block]:
ind_sol = self.sumk_to_solver[ish][(block,ind)]
if not ind_sol[0] in gfs[ish]:
gfs[ish][ind_sol[0]]=[]
gfs[ish][ind_sol[0]].append(ind_sol[1])
self.pick_gf_struct_solver(gfs)
def map_gf_struct_solver(self,mapping):
""" Map the Green function structure from one struct to another.
Parameters
----------
mapping : list of dict
the dict consists of elements
(from_block,from_index) : (to_block,to_index)
that maps from one structure to the other
"""
for ish in range(len(mapping)):
gf_struct = {}
so2su = {}
su2so = {}
so2su_block = {}
for frm,to in mapping[ish].iteritems():
if not to[0] in gf_struct:
gf_struct[to[0]]=[]
gf_struct[to[0]].append(to[1])
so2su[to]=self.solver_to_sumk[ish][frm]
su2so[self.solver_to_sumk[ish][frm]]=to
if to[0] in so2su_block:
if so2su_block[to[0]] != \
self.solver_to_sumk_block[ish][frm[0]]:
warn("solver block '{}' maps to more than one sumk block: '{}', '{}'".format(
to[0],so2su_block[to[0]],self.solver_to_sumk_block[ish][frm[0]]))
else:
so2su_block[to[0]]=\
self.solver_to_sumk_block[ish][frm[0]]
for k in self.sumk_to_solver[ish].keys():
if not k in su2so:
su2so[k] = (None,None)
self.gf_struct_solver[ish]=gf_struct
self.solver_to_sumk[ish]=so2su
self.sumk_to_solver[ish]=su2so
self.solver_to_sumk_block[ish]=so2su_block
def create_gf(self,ish=0,gf_function=GfImFreq,**kwargs):
""" Create a zero BlockGf having the gf_struct_solver structure.
When using GfImFreq as gf_function, typically you have to
supply beta as keyword argument.
Parameters
----------
ish : int
shell index
gf_function : constructor
function used to construct the Gf objects constituting the
individual blocks; default: GfImFreq
**kwargs :
options passed on to the Gf constructor for the individual
blocks
"""
names = self.gf_struct_solver[ish].keys()
blocks=[]
for n in names:
G = gf_function(indices=self.gf_struct_solver[ish][n],**kwargs)
blocks.append(G)
G = BlockGf(name_list = names, block_list = blocks)
return G
def convert_gf(self,G,G_struct,ish=0,show_warnings=True,**kwargs):
""" Convert BlockGf from its structure to this structure.
.. warning::
Elements that are zero in the new structure due to
the new block structure will be just ignored, thus
approximated to zero.
Parameters
----------
G : BlockGf
the Gf that should be converted
G_struct : GfStructure
the structure ofthat G
ish : int
shell index
show_warnings : bool
whether to show warnings when elements of the Green's
function get thrown away
**kwargs :
options passed to the constructor for the new Gf
"""
G_new = self.create_gf(ish=ish,**kwargs)
for block in G_struct.gf_struct_solver[ish].keys():
for i1 in G_struct.gf_struct_solver[ish][block]:
for i2 in G_struct.gf_struct_solver[ish][block]:
i1_sumk = G_struct.solver_to_sumk[ish][(block,i1)]
i2_sumk = G_struct.solver_to_sumk[ish][(block,i2)]
i1_sol = self.sumk_to_solver[ish][i1_sumk]
i2_sol = self.sumk_to_solver[ish][i2_sumk]
if i1_sol[0] is None or i2_sol[0] is None:
if show_warnings:
warn(('Element {},{} of block {} of G is not present '+
'in the new structure').format(i1,i2,block))
continue
if i1_sol[0]!=i2_sol[0]:
if show_warnings:
warn(('Element {},{} of block {} of G is approximated '+
'to zero to match the new structure.').format(
i1,i2,block))
continue
G_new[i1_sol[0]][i1_sol[1],i2_sol[1]] = \
G[block][i1,i2]
return G_new
def approximate_as_diagonal(self):
""" Create a structure for a GF with zero off-diagonal elements.
.. warning::
In general, this will throw away non-zero elements of the
Green's function. Be sure to verify whether this approximation
is justified.
"""
self.gf_struct_solver=[]
self.solver_to_sumk=[]
self.solver_to_sumk_block=[]
for ish in range(len(self.sumk_to_solver)):
self.gf_struct_solver.append({})
self.solver_to_sumk.append({})
self.solver_to_sumk_block.append({})
for frm,to in self.sumk_to_solver[ish].iteritems():
if to[0] is not None:
self.gf_struct_solver[ish][frm[0]+'_'+str(frm[1])]=[0]
self.sumk_to_solver[ish][frm]=(frm[0]+'_'+str(frm[1]),0)
self.solver_to_sumk[ish][(frm[0]+'_'+str(frm[1]),0)]=frm
self.solver_to_sumk_block[ish][frm[0]+'_'+str(frm[1])]=frm[0]
def __eq__(self,other):
def compare(one,two):
if type(one)!=type(two):
return False
if one is None and two is None:
return True
if isinstance(one,list) or isinstance(one,tuple):
if len(one) != len(two):
return False
for x,y in zip(one,two):
if not compare(x,y):
return False
return True
elif isinstance(one,int):
return one==two
elif isinstance(one,str):
return one==two
elif isinstance(one,dict):
if set(one.keys()) != set(two.keys()):
return False
for k in set(one.keys()).intersection(two.keys()):
if not compare(one[k],two[k]):
return False
return True
warn('Cannot compare {}'.format(type(one)))
return False
for prop in [ "gf_struct_sumk", "gf_struct_solver",
"solver_to_sumk", "sumk_to_solver", "solver_to_sumk_block"]:
if not compare(getattr(self,prop),getattr(other,prop)):
return False
return True
def copy(self):
return copy.deepcopy(self)
def __reduce_to_dict__(self):
""" Reduce to dict for HDF5 export."""
ret = {}
for element in [ "gf_struct_sumk", "gf_struct_solver",
"solver_to_sumk_block"]:
ret[element] = getattr(self,element)
def construct_mapping(mapping):
d = []
for ish in range(len(mapping)):
d.append({})
for k,v in mapping[ish].iteritems():
d[ish][repr(k)] = repr(v)
return d
ret['solver_to_sumk']=construct_mapping(self.solver_to_sumk)
ret['sumk_to_solver']=construct_mapping(self.sumk_to_solver)
return ret
@classmethod
def __factory_from_dict__(cls,name,D) :
""" Create from dict for HDF5 import."""
def reconstruct_mapping(mapping):
d = []
for ish in range(len(mapping)):
d.append({})
for k,v in mapping[ish].iteritems():
# literal_eval is a saje alternative to eval
d[ish][literal_eval(k)] = literal_eval(v)
return d
D['solver_to_sumk']=reconstruct_mapping(D['solver_to_sumk'])
D['sumk_to_solver']=reconstruct_mapping(D['sumk_to_solver'])
return cls(**D)
def __str__(self):
s=''
s+= "gf_struct_sumk "+str( self.gf_struct_sumk)+'\n'
s+= "gf_struct_solver "+str(self.gf_struct_solver)+'\n'
s+= "solver_to_sumk_block "+str(self.solver_to_sumk_block)+'\n'
for el in ['solver_to_sumk','sumk_to_solver']:
s+=el+'\n'
element=getattr(self,el)
for ish in range(len(element)):
s+=' shell '+str(ish)+'\n'
def keyfun(el):
return '{}_{:05d}'.format(el[0],el[1])
keys = sorted(element[ish].keys(),key=keyfun)
for k in keys:
s+=' '+str(k)+str(element[ish][k])+'\n'
return s
from pytriqs.archive.hdf_archive_schemes import register_class
register_class(BlockStructure)

9
python/clear_h5_output.py
View File

@ -13,13 +13,14 @@ and to restore it to the original post-converter state.
filename = sys.argv[1]
A = h5py.File(filename)
for group in ['dmft_output','user_data']:
if group in A: del(A[group])
for group in ['dmft_output', 'user_data']:
if group in A:
del(A[group])
A.close()
# Repack to reclaim disk space
retcode = subprocess.call(["h5repack","-i%s"%filename, "-otemphgfrt.h5"])
retcode = subprocess.call(["h5repack", "-i%s" % filename, "-otemphgfrt.h5"])
if retcode != 0:
print "h5repack failed!"
else:
subprocess.call(["mv","-f","temphgfrt.h5","%s"%filename])
subprocess.call(["mv", "-f", "temphgfrt.h5", "%s" % filename])

5
python/converters/__init__.py
View File

@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,7 +18,7 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
from wien2k_converter import Wien2kConverter
from hk_converter import HkConverter
@ -27,4 +27,3 @@ from wannier90_converter import Wannier90Converter
__all__ =['Wien2kConverter','HkConverter','Wannier90Converter','VaspConverter']

55
python/converters/converter_tools.py
View File

@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,13 +18,17 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
from pytriqs.cmake_info import hdf5_command_path
import pytriqs.utility.mpi as mpi
class ConverterTools:
def read_fortran_file(self,filename,to_replace):
def __init__(self):
pass
def read_fortran_file(self, filename, to_replace):
"""
Returns a generator that yields all numbers in the Fortran file as float, with possible replacements.
@ -43,11 +47,13 @@ class ConverterTools:
"""
import os.path
import string
if not(os.path.exists(filename)) : raise IOError, "File %s does not exist."%filename
for line in open(filename,'r') :
for old,new in to_replace.iteritems(): line = line.replace(old,new)
for x in line.split(): yield string.atof(x)
if not(os.path.exists(filename)):
raise IOError, "File %s does not exist." % filename
for line in open(filename, 'r'):
for old, new in to_replace.iteritems():
line = line.replace(old, new)
for x in line.split():
yield string.atof(x)
def repack(self):
"""
@ -62,17 +68,18 @@ class ConverterTools:
import subprocess
if not (mpi.is_master_node()): return
mpi.report("Repacking the file %s"%self.hdf_file)
if not (mpi.is_master_node()):
return
mpi.report("Repacking the file %s" % self.hdf_file)
retcode = subprocess.call([hdf5_command_path+"/h5repack","-i%s"%self.hdf_file,"-otemphgfrt.h5"])
retcode = subprocess.call(
[hdf5_command_path + "/h5repack", "-i%s" % self.hdf_file, "-otemphgfrt.h5"])
if retcode != 0:
mpi.report("h5repack failed!")
else:
subprocess.call(["mv","-f","temphgfrt.h5","%s"%self.hdf_file])
subprocess.call(["mv", "-f", "temphgfrt.h5", "%s" % self.hdf_file])
def det_shell_equivalence(self,corr_shells):
def det_shell_equivalence(self, corr_shells):
"""
Determine the equivalence of correlated shells.
@ -102,19 +109,19 @@ class ConverterTools:
n_inequiv_shells = 1
if len(corr_shells) > 1:
inequiv_sort = [ corr_shells[0]['sort'] ]
inequiv_l = [ corr_shells[0]['l'] ]
for i in range(len(corr_shells)-1):
inequiv_sort = [corr_shells[0]['sort']]
inequiv_l = [corr_shells[0]['l']]
for i in range(len(corr_shells) - 1):
is_equiv = False
for j in range(n_inequiv_shells):
if (inequiv_sort[j]==corr_shells[i+1]['sort']) and (inequiv_l[j]==corr_shells[i+1]['l']):
if (inequiv_sort[j] == corr_shells[i + 1]['sort']) and (inequiv_l[j] == corr_shells[i + 1]['l']):
is_equiv = True
corr_to_inequiv[i+1] = j
if is_equiv==False:
corr_to_inequiv[i+1] = n_inequiv_shells
corr_to_inequiv[i + 1] = j
if is_equiv == False:
corr_to_inequiv[i + 1] = n_inequiv_shells
n_inequiv_shells += 1
inequiv_sort.append( corr_shells[i+1]['sort'] )
inequiv_l.append( corr_shells[i+1]['l'] )
inequiv_to_corr.append( i+1 )
inequiv_sort.append(corr_shells[i + 1]['sort'])
inequiv_l.append(corr_shells[i + 1]['l'])
inequiv_to_corr.append(i + 1)
return n_inequiv_shells, corr_to_inequiv, inequiv_to_corr

174
python/converters/hk_converter.py
View File

@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,7 +18,7 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
from types import *
import numpy
@ -27,12 +27,13 @@ import pytriqs.utility.mpi as mpi
from math import sqrt
from converter_tools import *
class HkConverter(ConverterTools):
"""
Conversion from general H(k) file to an hdf5 file that can be used as input for the SumKDFT class.
"""
def __init__(self, filename, hdf_filename = None, dft_subgrp = 'dft_input', symmcorr_subgrp = 'dft_symmcorr_input', repacking = False):
def __init__(self, filename, hdf_filename=None, dft_subgrp='dft_input', symmcorr_subgrp='dft_symmcorr_input', repacking=False):
"""
Initialise the class.
@ -52,21 +53,22 @@ class HkConverter(ConverterTools):
"""
assert type(filename)==StringType,"HkConverter: filename must be a filename."
if hdf_filename is None: hdf_filename = filename+'.h5'
assert type(
filename) == StringType, "HkConverter: filename must be a filename."
if hdf_filename is None:
hdf_filename = filename + '.h5'
self.hdf_file = hdf_filename
self.dft_file = filename
self.dft_subgrp = dft_subgrp
self.symmcorr_subgrp = symmcorr_subgrp
self.fortran_to_replace = {'D':'E', '(':' ', ')':' ', ',':' '}
self.fortran_to_replace = {'D': 'E', '(': ' ', ')': ' ', ',': ' '}
# Checks if h5 file is there and repacks it if wanted:
import os.path
if (os.path.exists(self.hdf_file) and repacking):
ConverterTools.repack(self)
def convert_dft_input(self, first_real_part_matrix = True, only_upper_triangle = False, weights_in_file = False):
def convert_dft_input(self, first_real_part_matrix=True, only_upper_triangle=False, weights_in_file=False):
"""
Reads the appropriate files and stores the data for the dft_subgrp in the hdf5 archive.
@ -82,39 +84,55 @@ class HkConverter(ConverterTools):
"""
# Read and write only on the master node
if not (mpi.is_master_node()): return
mpi.report("Reading input from %s..."%self.dft_file)
if not (mpi.is_master_node()):
return
mpi.report("Reading input from %s..." % self.dft_file)
# R is a generator : each R.Next() will return the next number in the file
R = ConverterTools.read_fortran_file(self,self.dft_file,self.fortran_to_replace)
# R is a generator : each R.Next() will return the next number in the
# file
R = ConverterTools.read_fortran_file(
self, self.dft_file, self.fortran_to_replace)
try:
energy_unit = 1.0 # the energy conversion factor is 1.0, we assume eV in files
n_k = int(R.next()) # read the number of k points
# the energy conversion factor is 1.0, we assume eV in files
energy_unit = 1.0
# read the number of k points
n_k = int(R.next())
k_dep_projection = 0
SP = 0 # no spin-polarision
SO = 0 # no spin-orbit
charge_below = 0.0 # total charge below energy window is set to 0
density_required = R.next() # density required, for setting the chemical potential
# total charge below energy window is set to 0
charge_below = 0.0
# density required, for setting the chemical potential
density_required = R.next()
symm_op = 0 # No symmetry groups for the k-sum
# the information on the non-correlated shells is needed for defining dimension of matrices:
n_shells = int(R.next()) # number of shells considered in the Wanniers
# the information on the non-correlated shells is needed for
# defining dimension of matrices:
# number of shells considered in the Wanniers
n_shells = int(R.next())
# corresponds to index R in formulas
# now read the information about the shells (atom, sort, l, dim):
shell_entries = ['atom', 'sort', 'l', 'dim']
shells = [ {name: int(val) for name, val in zip(shell_entries, R)} for ish in range(n_shells) ]
shells = [{name: int(val) for name, val in zip(
shell_entries, R)} for ish in range(n_shells)]
n_corr_shells = int(R.next()) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
# number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
n_corr_shells = int(R.next())
# corresponds to index R in formulas
# now read the information about the shells (atom, sort, l, dim, SO flag, irep):
corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
corr_shells = [ {name: int(val) for name, val in zip(corr_shell_entries, R)} for icrsh in range(n_corr_shells) ]
# now read the information about the shells (atom, sort, l, dim, SO
# flag, irep):
corr_shell_entries = ['atom', 'sort', 'l', 'dim','SO','irep']
corr_shells = [{name: int(val) for name, val in zip(
corr_shell_entries, R)} for icrsh in range(n_corr_shells)]
# determine the number of inequivalent correlated shells and maps, needed for further reading
[n_inequiv_shells, corr_to_inequiv, inequiv_to_corr] = ConverterTools.det_shell_equivalence(self,corr_shells)
# determine the number of inequivalent correlated shells and maps,
# needed for further reading
[n_inequiv_shells, corr_to_inequiv,
inequiv_to_corr] = ConverterTools.det_shell_equivalence(self, corr_shells)
use_rotations = 0
rot_mat = [numpy.identity(corr_shells[icrsh]['dim'],numpy.complex_) for icrsh in range(n_corr_shells)]
rot_mat = [numpy.identity(
corr_shells[icrsh]['dim'], numpy.complex_) for icrsh in range(n_corr_shells)]
rot_mat_time_inv = [0 for i in range(n_corr_shells)]
# Representative representations are read from file
@ -122,29 +140,39 @@ class HkConverter(ConverterTools):
dim_reps = [0 for i in range(n_inequiv_shells)]
T = []
for ish in range(n_inequiv_shells):
n_reps[ish] = int(R.next()) # number of representatives ("subsets"), e.g. t2g and eg
dim_reps[ish] = [int(R.next()) for i in range(n_reps[ish])] # dimensions of the subsets
# number of representatives ("subsets"), e.g. t2g and eg
n_reps[ish] = int(R.next())
dim_reps[ish] = [int(R.next()) for i in range(
n_reps[ish])] # dimensions of the subsets
# The transformation matrix:
# is of dimension 2l+1, it is taken to be standard d (as in Wien2k)
ll = 2*corr_shells[inequiv_to_corr[ish]]['l']+1
# is of dimension 2l+1, it is taken to be standard d (as in
# Wien2k)
ll = 2 * corr_shells[inequiv_to_corr[ish]]['l'] + 1
lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
T.append(numpy.zeros([lmax,lmax],numpy.complex_))
T.append(numpy.zeros([lmax, lmax], numpy.complex_))
T[ish] = numpy.array([[0.0, 0.0, 1.0, 0.0, 0.0],
[1.0/sqrt(2.0), 0.0, 0.0, 0.0, 1.0/sqrt(2.0)],
[-1.0/sqrt(2.0), 0.0, 0.0, 0.0, 1.0/sqrt(2.0)],
[0.0, 1.0/sqrt(2.0), 0.0, -1.0/sqrt(2.0), 0.0],
[0.0, 1.0/sqrt(2.0), 0.0, 1.0/sqrt(2.0), 0.0]])
[1.0 / sqrt(2.0), 0.0, 0.0,
0.0, 1.0 / sqrt(2.0)],
[-1.0 / sqrt(2.0), 0.0, 0.0,
0.0, 1.0 / sqrt(2.0)],
[0.0, 1.0 /
sqrt(2.0), 0.0, -1.0 / sqrt(2.0), 0.0],
[0.0, 1.0 / sqrt(2.0), 0.0, 1.0 / sqrt(2.0), 0.0]])
# Spin blocks to be read:
n_spin_blocs = SP + 1 - SO # number of spins to read for Norbs and Ham, NOT Projectors
# number of spins to read for Norbs and Ham, NOT Projectors
n_spin_blocs = SP + 1 - SO
# define the number of n_orbitals for all k points: it is the number of total bands and independent of k!
n_orbitals = numpy.ones([n_k,n_spin_blocs],numpy.int) * sum([ sh['dim'] for sh in shells ])
# define the number of n_orbitals for all k points: it is the
# number of total bands and independent of k!
n_orbitals = numpy.ones(
[n_k, n_spin_blocs], numpy.int) * sum([sh['dim'] for sh in shells])
# Initialise the projectors:
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_)
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_)
# Read the projectors from the file:
for ik in range(n_k):
@ -155,21 +183,25 @@ class HkConverter(ConverterTools):
offset = 0
n_orb = 0
for ish in range(n_shells):
if (n_orb==0):
if (shells[ish]['atom']==corr_shells[icrsh]['atom']) and (shells[ish]['sort']==corr_shells[icrsh]['sort']):
if (n_orb == 0):
if (shells[ish]['atom'] == corr_shells[icrsh]['atom']) and (shells[ish]['sort'] == corr_shells[icrsh]['sort']):
n_orb = corr_shells[icrsh]['dim']
else:
offset += shells[ish]['dim']
proj_mat[ik,isp,icrsh,0:n_orb,offset:offset+n_orb] = numpy.identity(n_orb)
proj_mat[ik, isp, icrsh, 0:n_orb,
offset:offset + n_orb] = numpy.identity(n_orb)
# 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_)
# w(k_index), default normalisation
bz_weights = numpy.ones([n_k], numpy.float_) / float(n_k)
hopping = numpy.zeros([n_k, n_spin_blocs, max(
n_orbitals), max(n_orbitals)], numpy.complex_)
if (weights_in_file):
# weights in the file
for ik in range(n_k) : bz_weights[ik] = R.next()
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)
@ -177,27 +209,31 @@ class HkConverter(ConverterTools):
# Grab the H
for isp in range(n_spin_blocs):
for ik in range(n_k) :
n_orb = n_orbitals[ik,isp]
for ik in range(n_k):
n_orb = n_orbitals[ik, isp]
if (first_real_part_matrix): # first read all real components for given k, then read imaginary parts
# first read all real components for given k, then read
# imaginary parts
if (first_real_part_matrix):
for i in range(n_orb):
if (only_upper_triangle):
istart = i
else:
istart = 0
for j in range(istart,n_orb):
hopping[ik,isp,i,j] = R.next()
for j in range(istart, n_orb):
hopping[ik, isp, i, j] = R.next()
for i in range(n_orb):
if (only_upper_triangle):
istart = i
else:
istart = 0
for j in range(istart,n_orb):
hopping[ik,isp,i,j] += R.next() * 1j
if ((only_upper_triangle)and(i!=j)): hopping[ik,isp,j,i] = hopping[ik,isp,i,j].conjugate()
for j in range(istart, n_orb):
hopping[ik, isp, i, j] += R.next() * 1j
if ((only_upper_triangle)and(i != j)):
hopping[ik, isp, j, i] = hopping[
ik, isp, i, j].conjugate()
else: # read (real,im) tuple
@ -206,25 +242,31 @@ class HkConverter(ConverterTools):
istart = i
else:
istart = 0
for j in range(istart,n_orb):
hopping[ik,isp,i,j] = R.next()
hopping[ik,isp,i,j] += R.next() * 1j
for j in range(istart, n_orb):
hopping[ik, isp, i, j] = R.next()
hopping[ik, isp, i, j] += R.next() * 1j
if ((only_upper_triangle)and(i!=j)): hopping[ik,isp,j,i] = hopping[ik,isp,i,j].conjugate()
if ((only_upper_triangle)and(i != j)):
hopping[ik, isp, j, i] = hopping[
ik, isp, i, j].conjugate()
# 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.
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 "HK Converter : reading file dft_file failed!"
R.close()
# Save to the HDF5:
ar = HDFArchive(self.hdf_file,'a')
if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp)
things_to_save = ['energy_unit','n_k','k_dep_projection','SP','SO','charge_below','density_required',
'symm_op','n_shells','shells','n_corr_shells','corr_shells','use_rotations','rot_mat',
'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights','hopping',
ar = HDFArchive(self.hdf_file, 'a')
if not (self.dft_subgrp in ar):
ar.create_group(self.dft_subgrp)
things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required',
'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat',
'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping',
'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr']
for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it]
for it in things_to_save:
ar[self.dft_subgrp][it] = locals()[it]
del ar

102
python/converters/wannier90_converter.py
View File

@ -91,7 +91,8 @@ class Wannier90Converter(ConverterTools):
self.dft_subgrp = dft_subgrp
self.symmcorr_subgrp = symmcorr_subgrp
self.fortran_to_replace = {'D': 'E'}
# threshold below which matrix elements from wannier90 should be considered equal
# threshold below which matrix elements from wannier90 should be
# considered equal
self._w90zero = 2.e-6
# Checks if h5 file is there and repacks it if wanted:
@ -114,12 +115,14 @@ class Wannier90Converter(ConverterTools):
return
mpi.report("Reading input from %s..." % self.inp_file)
# R is a generator : each R.Next() will return the next number in the file
# R is a generator : each R.Next() will return the next number in the
# file
R = ConverterTools.read_fortran_file(
self, self.inp_file, self.fortran_to_replace)
shell_entries = ['atom', 'sort', 'l', 'dim']
corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
# First, let's read the input file with the parameters needed for the conversion
# First, let's read the input file with the parameters needed for the
# conversion
try:
# read k - point mesh generation option
kmesh_mode = int(R.next())
@ -135,7 +138,8 @@ class Wannier90Converter(ConverterTools):
# and the data will be copied from corr_shells into shells (see below)
# number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
n_corr_shells = int(R.next())
# now read the information about the correlated shells (atom, sort, l, dim, SO flag, irep):
# now read the information about the correlated shells (atom, sort,
# l, dim, SO flag, irep):
corr_shells = [{name: int(val) for name, val in zip(
corr_shell_entries, R)} for icrsh in range(n_corr_shells)]
except StopIteration: # a more explicit error if the file is corrupted.
@ -166,7 +170,8 @@ class Wannier90Converter(ConverterTools):
mpi.report(
"Total number of WFs expected in the correlated shells: %d" % dim_corr_shells)
# determine the number of inequivalent correlated shells and maps, needed for further processing
# determine the number of inequivalent correlated shells and maps,
# needed for further processing
n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(
self, corr_shells)
mpi.report("Number of inequivalent shells: %d" % n_inequiv_shells)
@ -176,7 +181,8 @@ class Wannier90Converter(ConverterTools):
mpi.report("Mapping: " + format(shells_map))
# build the k-point mesh, if its size was given on input (kmesh_mode >= 0),
# otherwise it is built according to the data in the hr file (see below)
# otherwise it is built according to the data in the hr file (see
# below)
if kmesh_mode >= 0:
n_k, k_mesh, bz_weights = self.kmesh_build(nki, kmesh_mode)
self.n_k = n_k
@ -197,7 +203,8 @@ class Wannier90Converter(ConverterTools):
# TODO: generalise to SP=1 (only partially done)
rot_mat_time_inv = [0 for i in range(n_corr_shells)]
# Second, let's read the file containing the Hamiltonian in WF basis produced by Wannier90
# Second, let's read the file containing the Hamiltonian in WF basis
# produced by Wannier90
for isp in range(n_spin):
# begin loop on isp
@ -212,20 +219,24 @@ class Wannier90Converter(ConverterTools):
mpi.report(
"The Hamiltonian in MLWF basis is extracted from %s ..." % hr_file)
nr, rvec, rdeg, nw, hamr = self.read_wannier90hr(hr_file)
# number of R vectors, their indices, their degeneracy, number of WFs, H(R)
# number of R vectors, their indices, their degeneracy, number of
# WFs, H(R)
mpi.report("... done: %d R vectors, %d WFs found" % (nr, nw))
if isp == 0:
# set or check some quantities that must be the same for both spins
# set or check some quantities that must be the same for both
# spins
self.nrpt = nr
# k-point grid: (if not defined before)
if kmesh_mode == -1:
# the size of the k-point mesh is determined from the largest R vector
# the size of the k-point mesh is determined from the
# largest R vector
nki = [2 * rvec[:, idir].max() + 1 for idir in range(3)]
# it will be the same as in the win only when nki is odd, because of the
# wannier90 convention: if we have nki k-points along the i-th direction,
# then we should get 2*(nki/2)+nki%2 R points along that direction
# then we should get 2*(nki/2)+nki%2 R points along that
# direction
n_k, k_mesh, bz_weights = self.kmesh_build(nki)
self.n_k = n_k
self.k_mesh = k_mesh
@ -237,33 +248,41 @@ class Wannier90Converter(ConverterTools):
self.nwfs = nw
# check that the total number of WFs makes sense
if self.nwfs < dim_corr_shells:
mpi.report("ERROR: number of WFs in the file smaller than number of correlated orbitals!")
mpi.report(
"ERROR: number of WFs in the file smaller than number of correlated orbitals!")
elif self.nwfs > dim_corr_shells:
# NOTE: correlated shells must appear before uncorrelated ones inside the file
# NOTE: correlated shells must appear before uncorrelated
# ones inside the file
mpi.report("Number of WFs larger than correlated orbitals:\n" +
"WFs from %d to %d treated as uncorrelated" % (dim_corr_shells + 1, self.nwfs))
else:
mpi.report("Number of WFs equal to number of correlated orbitals")
mpi.report(
"Number of WFs equal to number of correlated orbitals")
# we assume spin up and spin down always have same total number of WFs
# we assume spin up and spin down always have same total number
# of WFs
n_orbitals = numpy.ones(
[self.n_k, n_spin], numpy.int) * self.nwfs
else:
# consistency check between the _up and _down file contents
if nr != self.nrpt:
mpi.report("Different number of R vectors for spin-up/spin-down!")
mpi.report(
"Different number of R vectors for spin-up/spin-down!")
if nw != self.nwfs:
mpi.report("Different number of WFs for spin-up/spin-down!")
mpi.report(
"Different number of WFs for spin-up/spin-down!")
hamr_full.append(hamr)
# FIXME: when do we actually need deepcopy()?
# hamr_full.append(deepcopy(hamr))
for ir in range(nr):
# checks if the Hamiltonian is real (it should, if wannierisation worked fine)
# checks if the Hamiltonian is real (it should, if
# wannierisation worked fine)
if numpy.abs((hamr[ir].imag.max()).max()) > self._w90zero:
mpi.report("H(R) has large complex components at R %d" % ir)
mpi.report(
"H(R) has large complex components at R %d" % ir)
# copy the R=0 block corresponding to the correlated shells
# into another variable (needed later for finding rot_mat)
if rvec[ir, 0] == 0 and rvec[ir, 1] == 0 and rvec[ir, 2] == 0:
@ -273,17 +292,22 @@ class Wannier90Converter(ConverterTools):
if not numpy.allclose(ham_corr0.transpose().conjugate(), ham_corr0, atol=self._w90zero, rtol=1.e-9):
raise ValueError("H(R=0) matrix is not Hermitian!")
# find rot_mat symmetries by diagonalising the on-site Hamiltonian of the first spin
# find rot_mat symmetries by diagonalising the on-site Hamiltonian
# of the first spin
if isp == 0:
use_rotations, rot_mat = self.find_rot_mat(n_corr_shells, corr_shells, shells_map, ham_corr0)
use_rotations, rot_mat = self.find_rot_mat(
n_corr_shells, corr_shells, shells_map, ham_corr0)
else:
# consistency check
use_rotations_, rot_mat_ = self.find_rot_mat(n_corr_shells, corr_shells, shells_map, ham_corr0)
use_rotations_, rot_mat_ = self.find_rot_mat(
n_corr_shells, corr_shells, shells_map, ham_corr0)
if (use_rotations and not use_rotations_):
mpi.report("Rotations cannot be used for spin component n. %d" % isp)
mpi.report(
"Rotations cannot be used for spin component n. %d" % isp)
for icrsh in range(n_corr_shells):
if not numpy.allclose(rot_mat_[icrsh], rot_mat[icrsh], atol=self._w90zero, rtol=1.e-15):
mpi.report("Rotations for spin component n. %d do not match!" % isp)
mpi.report(
"Rotations for spin component n. %d do not match!" % isp)
# end loop on isp
mpi.report("The k-point grid has dimensions: %d, %d, %d" % tuple(nki))
@ -292,11 +316,14 @@ class Wannier90Converter(ConverterTools):
bz_weights = 0.5 * bz_weights
# Third, compute the hoppings in reciprocal space
hopping = numpy.zeros([self.n_k, n_spin, numpy.max(n_orbitals), numpy.max(n_orbitals)], numpy.complex_)
hopping = numpy.zeros([self.n_k, n_spin, numpy.max(
n_orbitals), numpy.max(n_orbitals)], numpy.complex_)
for isp in range(n_spin):
# make Fourier transform H(R) -> H(k) : it can be done one spin at a time
# make Fourier transform H(R) -> H(k) : it can be done one spin at
# a time
hamk = self.fourier_ham(self.nwfs, hamr_full[isp])
# copy the H(k) in the right place of hoppings... is there a better way to do this??
# copy the H(k) in the right place of hoppings... is there a better
# way to do this??
for ik in range(self.n_k):
#hopping[ik,isp,:,:] = deepcopy(hamk[ik][:,:])*energy_unit
hopping[ik, isp, :, :] = hamk[ik][:, :] * energy_unit
@ -309,7 +336,8 @@ class Wannier90Converter(ConverterTools):
# Projectors simply consist in identity matrix blocks selecting those MLWFs that
# correspond to the specific correlated shell indexed by icrsh.
# NOTE: we assume that the correlated orbitals appear at the beginning of the H(R)
# file and that the ordering of MLWFs matches the corr_shell info from the input.
# file and that the ordering of MLWFs matches the corr_shell info from
# the input.
for icrsh in range(n_corr_shells):
norb = corr_shells[icrsh]['dim']
proj_mat[:, :, icrsh, 0:norb, iorb:iorb +
@ -320,7 +348,8 @@ class Wannier90Converter(ConverterTools):
ar = HDFArchive(self.hdf_file, 'a')
if not (self.dft_subgrp in ar):
ar.create_group(self.dft_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
# The subgroup containing the data. If it does not exist, it is
# created. If it exists, the data is overwritten!
things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required',
'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat',
'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping',
@ -373,7 +402,8 @@ class Wannier90Converter(ConverterTools):
except ValueError:
mpi.report("Could not read number of WFs or R vectors")
# allocate arrays to save the R vector indexes and degeneracies and the Hamiltonian
# allocate arrays to save the R vector indexes and degeneracies and the
# Hamiltonian
rvec_idx = numpy.zeros((nrpt, 3), dtype=int)
rvec_deg = numpy.zeros(nrpt, dtype=int)
h_of_r = [numpy.zeros((num_wf, num_wf), dtype=numpy.complex_)
@ -383,7 +413,8 @@ class Wannier90Converter(ConverterTools):
currpos = 2
try:
ir = 0
# read the degeneracy of the R vectors (needed for the Fourier transform)
# read the degeneracy of the R vectors (needed for the Fourier
# transform)
while ir < nrpt:
currpos += 1
for x in hr_data[currpos].split():
@ -540,7 +571,8 @@ class Wannier90Converter(ConverterTools):
kmesh = numpy.zeros((nkpt, 3), dtype=float)
ii = 0
for ix, iy, iz in product(range(msize[0]), range(msize[1]), range(msize[2])):
kmesh[ii, :] = [float(ix) / msize[0], float(iy) / msize[1], float(iz) / msize[2]]
kmesh[ii, :] = [float(ix) / msize[0], float(iy) /
msize[1], float(iz) / msize[2]]
ii += 1
# weight is equal for all k-points because wannier90 uses uniform grid on whole BZ
# (normalization is always 1 and takes into account spin degeneracy)
@ -568,11 +600,13 @@ class Wannier90Converter(ConverterTools):
"""
twopi = 2 * numpy.pi
h_of_k = [numpy.zeros((norb, norb), dtype=numpy.complex_) for ik in range(self.n_k)]
h_of_k = [numpy.zeros((norb, norb), dtype=numpy.complex_)
for ik in range(self.n_k)]
ridx = numpy.array(range(self.nrpt))
for ik, ir in product(range(self.n_k), ridx):
rdotk = twopi * numpy.dot(self.k_mesh[ik], self.rvec[ir])
factor = (math.cos(rdotk) + 1j * math.sin(rdotk)) / float(self.rdeg[ir])
factor = (math.cos(rdotk) + 1j * math.sin(rdotk)) / \
float(self.rdeg[ir])
h_of_k[ik][:, :] += factor * h_of_r[ir][:, :]
return h_of_k

486
python/converters/wien2k_converter.py
View File

@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,7 +18,7 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
from types import *
import numpy
@ -26,16 +26,17 @@ from pytriqs.archive import *
from converter_tools import *
import os.path
class Wien2kConverter(ConverterTools):
"""
Conversion from Wien2k output to an hdf5 file that can be used as input for the SumkDFT class.
"""
def __init__(self, filename, hdf_filename = None,
dft_subgrp = 'dft_input', symmcorr_subgrp = 'dft_symmcorr_input',
def __init__(self, filename, hdf_filename=None,
dft_subgrp='dft_input', symmcorr_subgrp='dft_symmcorr_input',
parproj_subgrp='dft_parproj_input', symmpar_subgrp='dft_symmpar_input',
bands_subgrp = 'dft_bands_input', misc_subgrp = 'dft_misc_input',
transp_subgrp = 'dft_transp_input', repacking = False):
bands_subgrp='dft_bands_input', misc_subgrp='dft_misc_input',
transp_subgrp='dft_transp_input', repacking=False):
"""
Initialise the class.
@ -64,18 +65,20 @@ class Wien2kConverter(ConverterTools):
"""
assert type(filename)==StringType, "Wien2kConverter: Please provide the DFT files' base name as a string."
if hdf_filename is None: hdf_filename = filename+'.h5'
assert type(
filename) == StringType, "Wien2kConverter: Please provide the DFT files' base name as a string."
if hdf_filename is None:
hdf_filename = filename + '.h5'
self.hdf_file = hdf_filename
self.dft_file = filename+'.ctqmcout'
self.symmcorr_file = filename+'.symqmc'
self.parproj_file = filename+'.parproj'
self.symmpar_file = filename+'.sympar'
self.band_file = filename+'.outband'
self.bandwin_file = filename+'.oubwin'
self.struct_file = filename+'.struct'
self.outputs_file = filename+'.outputs'
self.pmat_file = filename+'.pmat'
self.dft_file = filename + '.ctqmcout'
self.symmcorr_file = filename + '.symqmc'
self.parproj_file = filename + '.parproj'
self.symmpar_file = filename + '.sympar'
self.band_file = filename + '.outband'
self.bandwin_file = filename + '.oubwin'
self.struct_file = filename + '.struct'
self.outputs_file = filename + '.outputs'
self.pmat_file = filename + '.pmat'
self.dft_subgrp = dft_subgrp
self.symmcorr_subgrp = symmcorr_subgrp
self.parproj_subgrp = parproj_subgrp
@ -83,13 +86,12 @@ class Wien2kConverter(ConverterTools):
self.bands_subgrp = bands_subgrp
self.misc_subgrp = misc_subgrp
self.transp_subgrp = transp_subgrp
self.fortran_to_replace = {'D':'E'}
self.fortran_to_replace = {'D': 'E'}
# Checks if h5 file is there and repacks it if wanted:
if (os.path.exists(self.hdf_file) and repacking):
ConverterTools.repack(self)
def convert_dft_input(self):
"""
Reads the appropriate files and stores the data for the
@ -103,39 +105,55 @@ class Wien2kConverter(ConverterTools):
"""
# Read and write only on the master node
if not (mpi.is_master_node()): return
mpi.report("Reading input from %s..."%self.dft_file)
if not (mpi.is_master_node()):
return
mpi.report("Reading input from %s..." % self.dft_file)
# R is a generator : each R.Next() will return the next number in the file
R = ConverterTools.read_fortran_file(self,self.dft_file,self.fortran_to_replace)
# R is a generator : each R.Next() will return the next number in the
# file
R = ConverterTools.read_fortran_file(
self, self.dft_file, self.fortran_to_replace)
try:
energy_unit = R.next() # read the energy convertion factor
n_k = int(R.next()) # read the number of k points
# read the number of k points
n_k = int(R.next())
k_dep_projection = 1
SP = int(R.next()) # flag for spin-polarised calculation
SO = int(R.next()) # flag for spin-orbit calculation
# flag for spin-polarised calculation
SP = int(R.next())
# flag for spin-orbit calculation
SO = int(R.next())
charge_below = R.next() # total charge below energy window
density_required = R.next() # total density required, for setting the chemical potential
# total density required, for setting the chemical potential
density_required = R.next()
symm_op = 1 # Use symmetry groups for the k-sum
# the information on the non-correlated shells is not important here, maybe skip:
n_shells = int(R.next()) # number of shells (e.g. Fe d, As p, O p) in the unit cell,
# the information on the non-correlated shells is not important
# here, maybe skip:
# number of shells (e.g. Fe d, As p, O p) in the unit cell,
n_shells = int(R.next())
# corresponds to index R in formulas
# now read the information about the shells (atom, sort, l, dim):
shell_entries = ['atom', 'sort', 'l', 'dim']
shells = [ {name: int(val) for name, val in zip(shell_entries, R)} for ish in range(n_shells) ]
shells = [{name: int(val) for name, val in zip(
shell_entries, R)} for ish in range(n_shells)]
n_corr_shells = int(R.next()) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
# number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
n_corr_shells = int(R.next())
# corresponds to index R in formulas
# now read the information about the shells (atom, sort, l, dim, SO flag, irep):
# now read the information about the shells (atom, sort, l, dim, SO
# flag, irep):
corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
corr_shells = [ {name: int(val) for name, val in zip(corr_shell_entries, R)} for icrsh in range(n_corr_shells) ]
corr_shells = [{name: int(val) for name, val in zip(
corr_shell_entries, R)} for icrsh in range(n_corr_shells)]
# determine the number of inequivalent correlated shells and maps, needed for further reading
n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self,corr_shells)
# determine the number of inequivalent correlated shells and maps,
# needed for further reading
n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(
self, corr_shells)
use_rotations = 1
rot_mat = [numpy.identity(corr_shells[icrsh]['dim'],numpy.complex_) for icrsh in range(n_corr_shells)]
rot_mat = [numpy.identity(
corr_shells[icrsh]['dim'], numpy.complex_) for icrsh in range(n_corr_shells)]
# read the matrices
rot_mat_time_inv = [0 for i in range(n_corr_shells)]
@ -143,12 +161,13 @@ class Wien2kConverter(ConverterTools):
for icrsh in range(n_corr_shells):
for i in range(corr_shells[icrsh]['dim']): # read real part:
for j in range(corr_shells[icrsh]['dim']):
rot_mat[icrsh][i,j] = R.next()
for i in range(corr_shells[icrsh]['dim']): # read imaginary part:
rot_mat[icrsh][i, j] = R.next()
# read imaginary part:
for i in range(corr_shells[icrsh]['dim']):
for j in range(corr_shells[icrsh]['dim']):
rot_mat[icrsh][i,j] += 1j * R.next()
rot_mat[icrsh][i, j] += 1j * R.next()
if (SP==1): # read time inversion flag:
if (SP == 1): # read time inversion flag:
rot_mat_time_inv[icrsh] = int(R.next())
# Read here the info for the transformation of the basis:
@ -156,94 +175,108 @@ class Wien2kConverter(ConverterTools):
dim_reps = [0 for i in range(n_inequiv_shells)]
T = []
for ish in range(n_inequiv_shells):
n_reps[ish] = int(R.next()) # number of representatives ("subsets"), e.g. t2g and eg
dim_reps[ish] = [int(R.next()) for i in range(n_reps[ish])] # dimensions of the subsets
# number of representatives ("subsets"), e.g. t2g and eg
n_reps[ish] = int(R.next())
dim_reps[ish] = [int(R.next()) for i in range(
n_reps[ish])] # dimensions of the subsets
# The transformation matrix:
# is of dimension 2l+1 without SO, and 2*(2l+1) with SO!
ll = 2*corr_shells[inequiv_to_corr[ish]]['l']+1
ll = 2 * corr_shells[inequiv_to_corr[ish]]['l'] + 1
lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
T.append(numpy.zeros([lmax,lmax],numpy.complex_))
T.append(numpy.zeros([lmax, lmax], numpy.complex_))
# now read it from file:
for i in range(lmax):
for j in range(lmax):
T[ish][i,j] = R.next()
T[ish][i, j] = R.next()
for i in range(lmax):
for j in range(lmax):
T[ish][i,j] += 1j * R.next()
T[ish][i, j] += 1j * R.next()
# Spin blocks to be read:
n_spin_blocs = SP + 1 - SO
# read the list of n_orbitals for all k points
n_orbitals = numpy.zeros([n_k,n_spin_blocs],numpy.int)
n_orbitals = numpy.zeros([n_k, n_spin_blocs], numpy.int)
for isp in range(n_spin_blocs):
for ik in range(n_k):
n_orbitals[ik,isp] = int(R.next())
n_orbitals[ik, isp] = int(R.next())
# Initialise the projectors:
proj_mat = numpy.zeros([n_k,n_spin_blocs,n_corr_shells,max([crsh['dim'] for crsh in corr_shells]),numpy.max(n_orbitals)],numpy.complex_)
proj_mat = numpy.zeros([n_k, n_spin_blocs, n_corr_shells, max(
[crsh['dim'] for crsh in corr_shells]), numpy.max(n_orbitals)], numpy.complex_)
# Read the projectors from the file:
for ik in range(n_k):
for icrsh in range(n_corr_shells):
n_orb = corr_shells[icrsh]['dim']
# first Real part for BOTH spins, due to conventions in dmftproj:
# first Real part for BOTH spins, due to conventions in
# dmftproj:
for isp in range(n_spin_blocs):
for i in range(n_orb):
for j in range(n_orbitals[ik][isp]):
proj_mat[ik,isp,icrsh,i,j] = R.next()
proj_mat[ik, isp, icrsh, i, j] = R.next()
# now Imag part:
for isp in range(n_spin_blocs):
for i in range(n_orb):
for j in range(n_orbitals[ik][isp]):
proj_mat[ik,isp,icrsh,i,j] += 1j * R.next()
proj_mat[ik, isp, icrsh, i, j] += 1j * R.next()
# 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,numpy.max(n_orbitals),numpy.max(n_orbitals)],numpy.complex_)
# w(k_index), default normalisation
bz_weights = numpy.ones([n_k], numpy.float_) / float(n_k)
hopping = numpy.zeros([n_k, n_spin_blocs, numpy.max(
n_orbitals), numpy.max(n_orbitals)], numpy.complex_)
# weights in the file
for ik in range(n_k) : bz_weights[ik] = R.next()
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.
# 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 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
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!"%self.dft_file
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!" % self.dft_file
R.close()
# Reading done!
# Save it to the HDF:
ar = HDFArchive(self.hdf_file,'a')
if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
things_to_save = ['energy_unit','n_k','k_dep_projection','SP','SO','charge_below','density_required',
'symm_op','n_shells','shells','n_corr_shells','corr_shells','use_rotations','rot_mat',
'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights','hopping',
ar = HDFArchive(self.hdf_file, 'a')
if not (self.dft_subgrp in ar):
ar.create_group(self.dft_subgrp)
# The subgroup containing the data. If it does not exist, it is
# created. If it exists, the data is overwritten!
things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required',
'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat',
'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping',
'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr']
for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it]
for it in things_to_save:
ar[self.dft_subgrp][it] = locals()[it]
del ar
# Symmetries are used, so now convert symmetry information for *correlated* orbitals:
self.convert_symmetry_input(orbits=self.corr_shells,symm_file=self.symmcorr_file,symm_subgrp=self.symmcorr_subgrp,SO=self.SO,SP=self.SP)
# Symmetries are used, so now convert symmetry information for
# *correlated* orbitals:
self.convert_symmetry_input(orbits=self.corr_shells, symm_file=self.symmcorr_file,
symm_subgrp=self.symmcorr_subgrp, SO=self.SO, SP=self.SP)
self.convert_misc_input()
def convert_parproj_input(self):
"""
Reads the appropriate files and stores the data for the
@ -255,31 +288,37 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
# get needed data from hdf file
ar = HDFArchive(self.hdf_file,'a')
things_to_read = ['SP','SO','n_shells','n_k','n_orbitals','shells']
ar = HDFArchive(self.hdf_file, 'a')
things_to_read = ['SP', 'SO', 'n_shells',
'n_k', 'n_orbitals', 'shells']
for it in things_to_read:
if not hasattr(self,it): setattr(self,it,ar[self.dft_subgrp][it])
if not hasattr(self, it):
setattr(self, it, ar[self.dft_subgrp][it])
self.n_spin_blocs = self.SP + 1 - self.SO
del ar
mpi.report("Reading input from %s..."%self.parproj_file)
mpi.report("Reading input from %s..." % self.parproj_file)
dens_mat_below = [ [numpy.zeros([self.shells[ish]['dim'],self.shells[ish]['dim']],numpy.complex_) for ish in range(self.n_shells)]
for isp in range(self.n_spin_blocs) ]
dens_mat_below = [[numpy.zeros([self.shells[ish]['dim'], self.shells[ish]['dim']], numpy.complex_) for ish in range(self.n_shells)]
for isp in range(self.n_spin_blocs)]
R = ConverterTools.read_fortran_file(self,self.parproj_file,self.fortran_to_replace)
R = ConverterTools.read_fortran_file(
self, self.parproj_file, self.fortran_to_replace)
n_parproj = [int(R.next()) for i in range(self.n_shells)]
n_parproj = numpy.array(n_parproj)
# Initialise P, here a double list of matrices:
proj_mat_all = numpy.zeros([self.n_k,self.n_spin_blocs,self.n_shells,max(n_parproj),max([sh['dim'] for sh in self.shells]),max(self.n_orbitals)],numpy.complex_)
proj_mat_all = numpy.zeros([self.n_k, self.n_spin_blocs, self.n_shells, max(
n_parproj), max([sh['dim'] for sh in self.shells]), max(self.n_orbitals)], numpy.complex_)
rot_mat_all = [numpy.identity(self.shells[ish]['dim'],numpy.complex_) for ish in range(self.n_shells)]
rot_mat_all = [numpy.identity(
self.shells[ish]['dim'], numpy.complex_) for ish in range(self.n_shells)]
rot_mat_all_time_inv = [0 for i in range(self.n_shells)]
for ish in range(self.n_shells):
@ -288,34 +327,39 @@ class Wien2kConverter(ConverterTools):
for ir in range(n_parproj[ish]):
for isp in range(self.n_spin_blocs):
for i in range(self.shells[ish]['dim']): # read real part:
# read real part:
for i in range(self.shells[ish]['dim']):
for j in range(self.n_orbitals[ik][isp]):
proj_mat_all[ik,isp,ish,ir,i,j] = R.next()
proj_mat_all[ik, isp, ish, ir, i, j] = R.next()
for isp in range(self.n_spin_blocs):
for i in range(self.shells[ish]['dim']): # read imaginary part:
# read imaginary part:
for i in range(self.shells[ish]['dim']):
for j in range(self.n_orbitals[ik][isp]):
proj_mat_all[ik,isp,ish,ir,i,j] += 1j * R.next()
proj_mat_all[ik, isp, ish,
ir, i, j] += 1j * R.next()
# now read the Density Matrix for this orbital below the energy window:
# now read the Density Matrix for this orbital below the energy
# window:
for isp in range(self.n_spin_blocs):
for i in range(self.shells[ish]['dim']): # read real part:
for j in range(self.shells[ish]['dim']):
dens_mat_below[isp][ish][i,j] = R.next()
dens_mat_below[isp][ish][i, j] = R.next()
for isp in range(self.n_spin_blocs):
for i in range(self.shells[ish]['dim']): # read imaginary part:
# read imaginary part:
for i in range(self.shells[ish]['dim']):
for j in range(self.shells[ish]['dim']):
dens_mat_below[isp][ish][i,j] += 1j * R.next()
if (self.SP==0): dens_mat_below[isp][ish] /= 2.0
dens_mat_below[isp][ish][i, j] += 1j * R.next()
if (self.SP == 0):
dens_mat_below[isp][ish] /= 2.0
# Global -> local rotation matrix for this shell:
for i in range(self.shells[ish]['dim']): # read real part:
for j in range(self.shells[ish]['dim']):
rot_mat_all[ish][i,j] = R.next()
rot_mat_all[ish][i, j] = R.next()
for i in range(self.shells[ish]['dim']): # read imaginary part:
for j in range(self.shells[ish]['dim']):
rot_mat_all[ish][i,j] += 1j * R.next()
rot_mat_all[ish][i, j] += 1j * R.next()
if (self.SP):
rot_mat_all_time_inv[ish] = int(R.next())
@ -324,16 +368,21 @@ class Wien2kConverter(ConverterTools):
# Reading done!
# Save it to the HDF:
ar = HDFArchive(self.hdf_file,'a')
if not (self.parproj_subgrp in ar): ar.create_group(self.parproj_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
things_to_save = ['dens_mat_below','n_parproj','proj_mat_all','rot_mat_all','rot_mat_all_time_inv']
for it in things_to_save: ar[self.parproj_subgrp][it] = locals()[it]
ar = HDFArchive(self.hdf_file, 'a')
if not (self.parproj_subgrp in ar):
ar.create_group(self.parproj_subgrp)
# The subgroup containing the data. If it does not exist, it is
# created. If it exists, the data is overwritten!
things_to_save = ['dens_mat_below', 'n_parproj',
'proj_mat_all', 'rot_mat_all', 'rot_mat_all_time_inv']
for it in things_to_save:
ar[self.parproj_subgrp][it] = locals()[it]
del ar
# Symmetries are used, so now convert symmetry information for *all* orbitals:
self.convert_symmetry_input(orbits=self.shells,symm_file=self.symmpar_file,symm_subgrp=self.symmpar_subgrp,SO=self.SO,SP=self.SP)
# Symmetries are used, so now convert symmetry information for *all*
# orbitals:
self.convert_symmetry_input(orbits=self.shells, symm_file=self.symmpar_file,
symm_subgrp=self.symmpar_subgrp, SO=self.SO, SP=self.SP)
def convert_bands_input(self):
"""
@ -341,94 +390,109 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
try:
# get needed data from hdf file
ar = HDFArchive(self.hdf_file,'a')
things_to_read = ['SP','SO','n_corr_shells','n_shells','corr_shells','shells','energy_unit']
ar = HDFArchive(self.hdf_file, 'a')
things_to_read = ['SP', 'SO', 'n_corr_shells',
'n_shells', 'corr_shells', 'shells', 'energy_unit']
for it in things_to_read:
if not hasattr(self,it): setattr(self,it,ar[self.dft_subgrp][it])
if not hasattr(self, it):
setattr(self, it, ar[self.dft_subgrp][it])
self.n_spin_blocs = self.SP + 1 - self.SO
del ar
mpi.report("Reading input from %s..."%self.band_file)
R = ConverterTools.read_fortran_file(self,self.band_file,self.fortran_to_replace)
mpi.report("Reading input from %s..." % self.band_file)
R = ConverterTools.read_fortran_file(
self, self.band_file, self.fortran_to_replace)
n_k = int(R.next())
# read the list of n_orbitals for all k points
n_orbitals = numpy.zeros([n_k,self.n_spin_blocs],numpy.int)
n_orbitals = numpy.zeros([n_k, self.n_spin_blocs], numpy.int)
for isp in range(self.n_spin_blocs):
for ik in range(n_k):
n_orbitals[ik,isp] = int(R.next())
n_orbitals[ik, isp] = int(R.next())
# Initialise the projectors:
proj_mat = numpy.zeros([n_k,self.n_spin_blocs,self.n_corr_shells,max([crsh['dim'] for crsh in self.corr_shells]),numpy.max(n_orbitals)],numpy.complex_)
proj_mat = numpy.zeros([n_k, self.n_spin_blocs, self.n_corr_shells, max(
[crsh['dim'] for crsh in self.corr_shells]), numpy.max(n_orbitals)], numpy.complex_)
# Read the projectors from the file:
for ik in range(n_k):
for icrsh in range(self.n_corr_shells):
n_orb = self.corr_shells[icrsh]['dim']
# first Real part for BOTH spins, due to conventions in dmftproj:
# first Real part for BOTH spins, due to conventions in
# dmftproj:
for isp in range(self.n_spin_blocs):
for i in range(n_orb):
for j in range(n_orbitals[ik,isp]):
proj_mat[ik,isp,icrsh,i,j] = R.next()
for j in range(n_orbitals[ik, isp]):
proj_mat[ik, isp, icrsh, i, j] = R.next()
# now Imag part:
for isp in range(self.n_spin_blocs):
for i in range(n_orb):
for j in range(n_orbitals[ik,isp]):
proj_mat[ik,isp,icrsh,i,j] += 1j * R.next()
for j in range(n_orbitals[ik, isp]):
proj_mat[ik, isp, icrsh, i, j] += 1j * R.next()
hopping = numpy.zeros([n_k,self.n_spin_blocs,numpy.max(n_orbitals),numpy.max(n_orbitals)],numpy.complex_)
hopping = numpy.zeros([n_k, self.n_spin_blocs, numpy.max(
n_orbitals), numpy.max(n_orbitals)], numpy.complex_)
# Grab the H
# we use now the convention of a DIAGONAL Hamiltonian!!!!
for isp in range(self.n_spin_blocs):
for ik in range(n_k) :
n_orb = n_orbitals[ik,isp]
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() * self.energy_unit
hopping[ik, isp, i, i] = R.next() * self.energy_unit
# now read the partial projectors:
n_parproj = [int(R.next()) for i in range(self.n_shells)]
n_parproj = numpy.array(n_parproj)
# Initialise P, here a double list of matrices:
proj_mat_all = numpy.zeros([n_k,self.n_spin_blocs,self.n_shells,max(n_parproj),max([sh['dim'] for sh in self.shells]),numpy.max(n_orbitals)],numpy.complex_)
proj_mat_all = numpy.zeros([n_k, self.n_spin_blocs, self.n_shells, max(n_parproj), max(
[sh['dim'] for sh in self.shells]), numpy.max(n_orbitals)], numpy.complex_)
for ish in range(self.n_shells):
for ik in range(n_k):
for ir in range(n_parproj[ish]):
for isp in range(self.n_spin_blocs):
for i in range(self.shells[ish]['dim']): # read real part:
for j in range(n_orbitals[ik,isp]):
proj_mat_all[ik,isp,ish,ir,i,j] = R.next()
# read real part:
for i in range(self.shells[ish]['dim']):
for j in range(n_orbitals[ik, isp]):
proj_mat_all[ik, isp, ish,
ir, i, j] = R.next()
for i in range(self.shells[ish]['dim']): # read imaginary part:
for j in range(n_orbitals[ik,isp]):
proj_mat_all[ik,isp,ish,ir,i,j] += 1j * R.next()
# read imaginary part:
for i in range(self.shells[ish]['dim']):
for j in range(n_orbitals[ik, isp]):
proj_mat_all[ik, isp, ish,
ir, i, j] += 1j * R.next()
R.close()
except KeyError:
raise "convert_bands_input : Needed data not found in hdf file. Consider calling convert_dft_input first!"
except StopIteration : # a more explicit error if the file is corrupted.
except StopIteration: # a more explicit error if the file is corrupted.
raise "Wien2k_converter : reading file band_file failed!"
# Reading done!
# Save it to the HDF:
ar = HDFArchive(self.hdf_file,'a')
if not (self.bands_subgrp in ar): ar.create_group(self.bands_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
things_to_save = ['n_k','n_orbitals','proj_mat','hopping','n_parproj','proj_mat_all']
for it in things_to_save: ar[self.bands_subgrp][it] = locals()[it]
ar = HDFArchive(self.hdf_file, 'a')
if not (self.bands_subgrp in ar):
ar.create_group(self.bands_subgrp)
# The subgroup containing the data. If it does not exist, it is
# created. If it exists, the data is overwritten!
things_to_save = ['n_k', 'n_orbitals', 'proj_mat',
'hopping', 'n_parproj', 'proj_mat_all']
for it in things_to_save:
ar[self.bands_subgrp][it] = locals()[it]
del ar
def convert_misc_input(self):
"""
Reads additional information on:
@ -442,11 +506,13 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
# Check if SP, SO and n_k are already in h5
ar = HDFArchive(self.hdf_file, 'r')
if not (self.dft_subgrp in ar): raise IOError, "convert_misc_input: No %s subgroup in hdf file found! Call convert_dft_input first." %self.dft_subgrp
if not (self.dft_subgrp in ar):
raise IOError, "convert_misc_input: No %s subgroup in hdf file found! Call convert_dft_input first." % self.dft_subgrp
SP = ar[self.dft_subgrp]['SP']
SO = ar[self.dft_subgrp]['SO']
n_k = ar[self.dft_subgrp]['n_k']
@ -462,25 +528,28 @@ class Wien2kConverter(ConverterTools):
if (SP == 0 or SO == 1):
files = [self.bandwin_file]
elif SP == 1:
files = [self.bandwin_file+'up', self.bandwin_file+'dn']
files = [self.bandwin_file + 'up', self.bandwin_file + 'dn']
else: # SO and SP can't both be 1
assert 0, "convert_misc_input: Reading oubwin error! Check SP and SO!"
band_window = [None for isp in range(SP + 1 - SO)]
for isp, f in enumerate(files):
if os.path.exists(f):
mpi.report("Reading input from %s..."%f)
R = ConverterTools.read_fortran_file(self, f, self.fortran_to_replace)
mpi.report("Reading input from %s..." % f)
R = ConverterTools.read_fortran_file(
self, f, self.fortran_to_replace)
n_k_oubwin = int(R.next())
if (n_k_oubwin != n_k):
mpi.report("convert_misc_input : WARNING : n_k in case.oubwin is different from n_k in case.klist")
assert int(R.next()) == SO, "convert_misc_input: SO is inconsistent in oubwin file!"
mpi.report(
"convert_misc_input : WARNING : n_k in case.oubwin is different from n_k in case.klist")
assert int(
R.next()) == SO, "convert_misc_input: SO is inconsistent in oubwin file!"
band_window[isp] = numpy.zeros((n_k_oubwin, 2), dtype=int)
for ik in xrange(n_k_oubwin):
R.next()
band_window[isp][ik,0] = R.next() # lowest band
band_window[isp][ik,1] = R.next() # highest band
band_window[isp][ik, 0] = R.next() # lowest band
band_window[isp][ik, 1] = R.next() # highest band
R.next()
things_to_save.append('band_window')
@ -493,7 +562,7 @@ class Wien2kConverter(ConverterTools):
# lattice_angles: unit cell angles in rad
if (os.path.exists(self.struct_file)):
mpi.report("Reading input from %s..."%self.struct_file)
mpi.report("Reading input from %s..." % self.struct_file)
with open(self.struct_file) as R:
try:
@ -501,31 +570,36 @@ class Wien2kConverter(ConverterTools):
lattice_type = R.readline().split()[0]
R.readline()
temp = R.readline()
lattice_constants = numpy.array([float(temp[0+10*i:10+10*i].strip()) for i in range(3)])
lattice_angles = numpy.array([float(temp[30+10*i:40+10*i].strip()) for i in range(3)]) * numpy.pi / 180.0
things_to_save.extend(['lattice_type', 'lattice_constants', 'lattice_angles'])
lattice_constants = numpy.array(
[float(temp[0 + 10 * i:10 + 10 * i].strip()) for i in range(3)])
lattice_angles = numpy.array(
[float(temp[30 + 10 * i:40 + 10 * i].strip()) for i in range(3)]) * numpy.pi / 180.0
things_to_save.extend(
['lattice_type', 'lattice_constants', 'lattice_angles'])
except IOError:
raise "convert_misc_input: reading file %s failed" %self.struct_file
raise "convert_misc_input: reading file %s failed" % self.struct_file
# Read relevant data from .outputs file
#######################################
# rot_symmetries: matrix representation of all (space group) symmetry operations
# rot_symmetries: matrix representation of all (space group) symmetry
# operations
if (os.path.exists(self.outputs_file)):
mpi.report("Reading input from %s..."%self.outputs_file)
mpi.report("Reading input from %s..." % self.outputs_file)
rot_symmetries = []
with open(self.outputs_file) as R:
try:
while 1:
temp = R.readline().strip(' ').split()
if (temp[0] =='PGBSYM:'):
if (temp[0] == 'PGBSYM:'):
n_symmetries = int(temp[-1])
break
for i in range(n_symmetries):
while 1:
if (R.readline().strip().split()[0] == 'Symmetry'): break
sym_i = numpy.zeros((3, 3), dtype = float)
if (R.readline().strip().split()[0] == 'Symmetry'):
break
sym_i = numpy.zeros((3, 3), dtype=float)
for ir in range(3):
temp = R.readline().strip().split()
for ic in range(3):
@ -535,15 +609,16 @@ class Wien2kConverter(ConverterTools):
things_to_save.extend(['n_symmetries', 'rot_symmetries'])
things_to_save.append('rot_symmetries')
except IOError:
raise "convert_misc_input: reading file %s failed" %self.outputs_file
raise "convert_misc_input: reading file %s failed" % self.outputs_file
# Save it to the HDF:
ar = HDFArchive(self.hdf_file,'a')
if not (self.misc_subgrp in ar): ar.create_group(self.misc_subgrp)
for it in things_to_save: ar[self.misc_subgrp][it] = locals()[it]
ar = HDFArchive(self.hdf_file, 'a')
if not (self.misc_subgrp in ar):
ar.create_group(self.misc_subgrp)
for it in things_to_save:
ar[self.misc_subgrp][it] = locals()[it]
del ar
def convert_transport_input(self):
"""
Reads the necessary information for transport calculations on:
@ -554,11 +629,13 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
# Check if SP, SO and n_k are already in h5
ar = HDFArchive(self.hdf_file, 'r')
if not (self.dft_subgrp in ar): raise IOError, "convert_transport_input: No %s subgroup in hdf file found! Call convert_dft_input first." %self.dft_subgrp
if not (self.dft_subgrp in ar):
raise IOError, "convert_transport_input: No %s subgroup in hdf file found! Call convert_dft_input first." % self.dft_subgrp
SP = ar[self.dft_subgrp]['SP']
SO = ar[self.dft_subgrp]['SO']
n_k = ar[self.dft_subgrp]['n_k']
@ -574,17 +651,19 @@ class Wien2kConverter(ConverterTools):
if (SP == 0 or SO == 1):
files = [self.pmat_file]
elif SP == 1:
files = [self.pmat_file+'up', self.pmat_file+'dn']
files = [self.pmat_file + 'up', self.pmat_file + 'dn']
else: # SO and SP can't both be 1
assert 0, "convert_transport_input: Reading velocity file error! Check SP and SO!"
velocities_k = [[] for f in files]
band_window_optics = []
for isp, f in enumerate(files):
if not os.path.exists(f) : raise IOError, "convert_transport_input: File %s does not exist" %f
mpi.report("Reading input from %s..."%f)
if not os.path.exists(f):
raise IOError, "convert_transport_input: File %s does not exist" % f
mpi.report("Reading input from %s..." % f)
R = ConverterTools.read_fortran_file(self, f, {'D':'E','(':'',')':'',',':' '})
R = ConverterTools.read_fortran_file(
self, f, {'D': 'E', '(': '', ')': '', ',': ' '})
band_window_optics_isp = []
for ik in xrange(n_k):
R.next()
@ -592,26 +671,34 @@ class Wien2kConverter(ConverterTools):
nu2 = int(R.next())
band_window_optics_isp.append((nu1, nu2))
n_bands = nu2 - nu1 + 1
for _ in range(4): R.next()
for _ in range(4):
R.next()
if n_bands <= 0:
velocity_xyz = numpy.zeros((1, 1, 3), dtype = complex)
velocity_xyz = numpy.zeros((1, 1, 3), dtype=complex)
else:
velocity_xyz = numpy.zeros((n_bands, n_bands, 3), dtype = complex)
velocity_xyz = numpy.zeros(
(n_bands, n_bands, 3), dtype=complex)
for nu_i in range(n_bands):
for nu_j in range(nu_i, n_bands):
for i in range(3):
velocity_xyz[nu_i][nu_j][i] = R.next() + R.next()*1j
if (nu_i != nu_j): velocity_xyz[nu_j][nu_i][i] = velocity_xyz[nu_i][nu_j][i].conjugate()
velocity_xyz[nu_i][nu_j][
i] = R.next() + R.next() * 1j
if (nu_i != nu_j):
velocity_xyz[nu_j][nu_i][i] = velocity_xyz[
nu_i][nu_j][i].conjugate()
velocities_k[isp].append(velocity_xyz)
band_window_optics.append(numpy.array(band_window_optics_isp))
R.close() # Reading done!
# Put data to HDF5 file
ar = HDFArchive(self.hdf_file, 'a')
if not (self.transp_subgrp in ar): ar.create_group(self.transp_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!!!
if not (self.transp_subgrp in ar):
ar.create_group(self.transp_subgrp)
# The subgroup containing the data. If it does not exist, it is
# created. If it exists, the data is overwritten!!!
things_to_save = ['band_window_optics', 'velocities_k']
for it in things_to_save: ar[self.transp_subgrp][it] = locals()[it]
for it in things_to_save:
ar[self.transp_subgrp][it] = locals()[it]
del ar
def convert_symmetry_input(self, orbits, symm_file, symm_subgrp, SO, SP):
@ -635,59 +722,70 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
mpi.report("Reading input from %s..."%symm_file)
if not (mpi.is_master_node()):
return
mpi.report("Reading input from %s..." % symm_file)
n_orbits = len(orbits)
R = ConverterTools.read_fortran_file(self,symm_file,self.fortran_to_replace)
R = ConverterTools.read_fortran_file(
self, symm_file, self.fortran_to_replace)
try:
n_symm = int(R.next()) # Number of symmetry operations
n_atoms = int(R.next()) # number of atoms involved
perm = [ [int(R.next()) for i in range(n_atoms)] for j in range(n_symm) ] # list of permutations of the atoms
perm = [[int(R.next()) for i in range(n_atoms)]
for j in range(n_symm)] # list of permutations of the atoms
if SP:
time_inv = [ int(R.next()) for j in range(n_symm) ] # time inversion for SO coupling
# time inversion for SO coupling
time_inv = [int(R.next()) for j in range(n_symm)]
else:
time_inv = [ 0 for j in range(n_symm) ]
time_inv = [0 for j in range(n_symm)]
# Now read matrices:
mat = []
for i_symm in range(n_symm):
mat.append( [ numpy.zeros([orbits[orb]['dim'], orbits[orb]['dim']],numpy.complex_) for orb in range(n_orbits) ] )
mat.append([numpy.zeros([orbits[orb]['dim'], orbits[orb][
'dim']], numpy.complex_) for orb in range(n_orbits)])
for orb in range(n_orbits):
for i in range(orbits[orb]['dim']):
for j in range(orbits[orb]['dim']):
mat[i_symm][orb][i,j] = R.next() # real part
# real part
mat[i_symm][orb][i, j] = R.next()
for i in range(orbits[orb]['dim']):
for j in range(orbits[orb]['dim']):
mat[i_symm][orb][i,j] += 1j * R.next() # imaginary part
mat[i_symm][orb][i, j] += 1j * \
R.next() # imaginary part
mat_tinv = [numpy.identity(orbits[orb]['dim'],numpy.complex_)
mat_tinv = [numpy.identity(orbits[orb]['dim'], numpy.complex_)
for orb in range(n_orbits)]
if ((SO==0) and (SP==0)):
# here we need an additional time inversion operation, so read it:
if ((SO == 0) and (SP == 0)):
# here we need an additional time inversion operation, so read
# it:
for orb in range(n_orbits):
for i in range(orbits[orb]['dim']):
for j in range(orbits[orb]['dim']):
mat_tinv[orb][i,j] = R.next() # real part
# real part
mat_tinv[orb][i, j] = R.next()
for i in range(orbits[orb]['dim']):
for j in range(orbits[orb]['dim']):
mat_tinv[orb][i,j] += 1j * R.next() # imaginary part
mat_tinv[orb][i, j] += 1j * \
R.next() # imaginary part
except StopIteration : # a more explicit error if the file is corrupted.
except StopIteration: # a more explicit error if the file is corrupted.
raise "Wien2k_converter : reading file symm_file failed!"
R.close()
# Reading done!
# Save it to the HDF:
ar = HDFArchive(self.hdf_file,'a')
if not (symm_subgrp in ar): ar.create_group(symm_subgrp)
things_to_save = ['n_symm','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
for it in things_to_save: ar[symm_subgrp][it] = locals()[it]
ar = HDFArchive(self.hdf_file, 'a')
if not (symm_subgrp in ar):
ar.create_group(symm_subgrp)
things_to_save = ['n_symm', 'n_atoms', 'perm',
'orbits', 'SO', 'SP', 'time_inv', 'mat', 'mat_tinv']
for it in things_to_save:
ar[symm_subgrp][it] = locals()[it]
del ar

891
python/sumk_dft.py
View File

File diff suppressed because it is too large Load Diff

546
python/sumk_dft_tools.py
View File

@ -1,4 +1,4 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -17,7 +17,7 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
import sys
from types import *
import numpy
@ -28,15 +28,15 @@ from sumk_dft import SumkDFT
from scipy.integrate import *
from scipy.interpolate import *
class SumkDFTTools(SumkDFT):
"""
Extends the SumkDFT class with some tools for analysing the data.
"""
def __init__(self, hdf_file, h_field = 0.0, use_dft_blocks = False, dft_data = 'dft_input', symmcorr_data = 'dft_symmcorr_input',
parproj_data = 'dft_parproj_input', symmpar_data = 'dft_symmpar_input', bands_data = 'dft_bands_input',
transp_data = 'dft_transp_input', misc_data = 'dft_misc_input'):
def __init__(self, hdf_file, h_field=0.0, use_dft_blocks=False, dft_data='dft_input', symmcorr_data='dft_symmcorr_input',
parproj_data='dft_parproj_input', symmpar_data='dft_symmpar_input', bands_data='dft_bands_input',
transp_data='dft_transp_input', misc_data='dft_misc_input'):
"""
Initialisation of the class. Parameters are exactly as for SumKDFT.
"""
@ -46,7 +46,6 @@ class SumkDFTTools(SumkDFT):
symmpar_data=symmpar_data, bands_data=bands_data, transp_data=transp_data,
misc_data=misc_data)
# Uses .data of only GfReFreq objects.
def dos_wannier_basis(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True):
"""
@ -84,86 +83,108 @@ class SumkDFTTools(SumkDFT):
om_min = om_mesh[0]
om_max = om_mesh[-1]
n_om = len(om_mesh)
mesh = (om_min,om_max,n_om)
mesh = (om_min, om_max, n_om)
else:
om_min,om_max,n_om = mesh
om_min, om_max, n_om = mesh
om_mesh = numpy.linspace(om_min, om_max, n_om)
G_loc = []
for icrsh in range(self.n_corr_shells):
spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
glist = [ GfReFreq(indices = inner, window = (om_min,om_max), n_points = n_om) for block,inner in self.gf_struct_sumk[icrsh]]
G_loc.append(BlockGf(name_list = spn, block_list = glist, make_copies=False))
for icrsh in range(self.n_corr_shells): G_loc[icrsh].zero()
glist = [GfReFreq(indices=inner, window=(om_min, om_max), n_points=n_om)
for block, inner in self.gf_struct_sumk[icrsh]]
G_loc.append(
BlockGf(name_list=spn, block_list=glist, make_copies=False))
for icrsh in range(self.n_corr_shells):
G_loc[icrsh].zero()
DOS = { sp: numpy.zeros([n_om],numpy.float_) for sp in self.spin_block_names[self.SO] }
DOSproj = [ {} for ish in range(self.n_inequiv_shells) ]
DOSproj_orb = [ {} for ish in range(self.n_inequiv_shells) ]
DOS = {sp: numpy.zeros([n_om], numpy.float_)
for sp in self.spin_block_names[self.SO]}
DOSproj = [{} for ish in range(self.n_inequiv_shells)]
DOSproj_orb = [{} for ish in range(self.n_inequiv_shells)]
for ish in range(self.n_inequiv_shells):
for sp in self.spin_block_names[self.corr_shells[self.inequiv_to_corr[ish]]['SO']]:
dim = self.corr_shells[self.inequiv_to_corr[ish]]['dim']
DOSproj[ish][sp] = numpy.zeros([n_om],numpy.float_)
DOSproj_orb[ish][sp] = numpy.zeros([n_om,dim,dim],numpy.float_)
DOSproj[ish][sp] = numpy.zeros([n_om], numpy.float_)
DOSproj_orb[ish][sp] = numpy.zeros(
[n_om, dim, dim], numpy.complex_)
ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(ik=ik,mu=mu,iw_or_w="w",broadening=broadening,mesh=mesh,with_Sigma=with_Sigma,with_dc=with_dc)
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_w *= self.bz_weights[ik]
# Non-projected DOS
for iom in range(n_om):
for bname,gf in G_latt_w:
DOS[bname][iom] -= gf.data[iom,:,:].imag.trace()/numpy.pi
for bname, gf in G_latt_w:
DOS[bname][iom] -= gf.data[iom, :, :].imag.trace() / \
numpy.pi
# Projected DOS:
for icrsh in range(self.n_corr_shells):
tmp = G_loc[icrsh].copy()
for bname,gf in tmp: tmp[bname] << self.downfold(ik,icrsh,bname,G_latt_w[bname],gf) # downfolding G
for bname, gf in tmp:
tmp[bname] << self.downfold(ik, icrsh, bname, G_latt_w[
bname], gf) # downfolding G
G_loc[icrsh] += tmp
# Collect data from mpi:
for bname in DOS:
DOS[bname] = mpi.all_reduce(mpi.world, DOS[bname], lambda x,y : x+y)
DOS[bname] = mpi.all_reduce(
mpi.world, DOS[bname], lambda x, y: x + y)
for icrsh in range(self.n_corr_shells):
G_loc[icrsh] << mpi.all_reduce(mpi.world, G_loc[icrsh], lambda x,y : x+y)
G_loc[icrsh] << mpi.all_reduce(
mpi.world, G_loc[icrsh], lambda x, y: x + y)
mpi.barrier()
# Symmetrize and rotate to local coord. system if needed:
if self.symm_op != 0: G_loc = self.symmcorr.symmetrize(G_loc)
if self.symm_op != 0:
G_loc = self.symmcorr.symmetrize(G_loc)
if self.use_rotations:
for icrsh in range(self.n_corr_shells):
for bname,gf in G_loc[icrsh]: G_loc[icrsh][bname] << self.rotloc(icrsh,gf,direction='toLocal')
for bname, gf in G_loc[icrsh]:
G_loc[icrsh][bname] << self.rotloc(
icrsh, gf, direction='toLocal')
# G_loc can now also be used to look at orbitally-resolved quantities
for ish in range(self.n_inequiv_shells):
for bname,gf in G_loc[self.inequiv_to_corr[ish]]: # loop over spins
for iom in range(n_om): DOSproj[ish][bname][iom] -= gf.data[iom,:,:].imag.trace()/numpy.pi
DOSproj_orb[ish][bname][:,:,:] -= gf.data[:,:,:].imag/numpy.pi
for bname, gf in G_loc[self.inequiv_to_corr[ish]]: # loop over spins
for iom in range(n_om):
DOSproj[ish][bname][iom] -= gf.data[iom,
:, :].imag.trace() / numpy.pi
DOSproj_orb[ish][bname][
:, :, :] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:,:,:]
# Write to files
if save_to_file and mpi.is_master_node():
for sp in self.spin_block_names[self.SO]:
f = open('DOS_wann_%s.dat'%sp, 'w')
for iom in range(n_om): f.write("%s %s\n"%(om_mesh[iom],DOS[sp][iom]))
f = open('DOS_wann_%s.dat' % sp, 'w')
for iom in range(n_om):
f.write("%s %s\n" % (om_mesh[iom], DOS[sp][iom]))
f.close()
# Partial
for ish in range(self.n_inequiv_shells):
f = open('DOS_wann_%s_proj%s.dat'%(sp,ish),'w')
for iom in range(n_om): f.write("%s %s\n"%(om_mesh[iom],DOSproj[ish][sp][iom]))
f = open('DOS_wann_%s_proj%s.dat' % (sp, ish), 'w')
for iom in range(n_om):
f.write("%s %s\n" %
(om_mesh[iom], DOSproj[ish][sp][iom]))
f.close()
# Orbitally-resolved
for i in range(self.corr_shells[self.inequiv_to_corr[ish]]['dim']):
for j in range(i,self.corr_shells[self.inequiv_to_corr[ish]]['dim']):
f = open('DOS_wann_'+sp+'_proj'+str(ish)+'_'+str(i)+'_'+str(j)+'.dat','w')
for iom in range(n_om): f.write("%s %s\n"%(om_mesh[iom],DOSproj_orb[ish][sp][iom,i,j]))
for j in range(i, self.corr_shells[self.inequiv_to_corr[ish]]['dim']):
f = open('DOS_wann_' + sp + '_proj' + str(ish) +
'_' + str(i) + '_' + str(j) + '.dat', 'w')
for iom in range(n_om):
f.write("%s %s %s\n" % (
om_mesh[iom], DOSproj_orb[ish][sp][iom, i, j].real,DOSproj_orb[ish][sp][iom, i, j].imag))
f.close()
return DOS, DOSproj, DOSproj_orb
# Uses .data of only GfReFreq objects.
def dos_parproj_basis(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True):
"""
@ -196,11 +217,14 @@ class SumkDFTTools(SumkDFT):
DOS projected to atoms and resolved into orbital contributions.
"""
things_to_read = ['n_parproj','proj_mat_all','rot_mat_all','rot_mat_all_time_inv']
value_read = self.read_input_from_hdf(subgrp=self.parproj_data,things_to_read = things_to_read)
if not value_read: return value_read
if self.symm_op: self.symmpar = Symmetry(self.hdf_file,subgroup=self.symmpar_data)
things_to_read = ['n_parproj', 'proj_mat_all',
'rot_mat_all', 'rot_mat_all_time_inv']
value_read = self.read_input_from_hdf(
subgrp=self.parproj_data, things_to_read=things_to_read)
if not value_read:
return value_read
if self.symm_op:
self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data)
if (mesh is None) and (not with_Sigma):
raise ValueError, "lattice_gf: Give the mesh=(om_min,om_max,n_points) for the lattice GfReFreq."
@ -209,91 +233,113 @@ class SumkDFTTools(SumkDFT):
om_min = om_mesh[0]
om_max = om_mesh[-1]
n_om = len(om_mesh)
mesh = (om_min,om_max,n_om)
mesh = (om_min, om_max, n_om)
else:
om_min,om_max,n_om = mesh
om_min, om_max, n_om = mesh
om_mesh = numpy.linspace(om_min, om_max, n_om)
G_loc = []
spn = self.spin_block_names[self.SO]
gf_struct_parproj = [ [ (sp, range(self.shells[ish]['dim'])) for sp in spn ]
for ish in range(self.n_shells) ]
gf_struct_parproj = [[(sp, range(self.shells[ish]['dim'])) for sp in spn]
for ish in range(self.n_shells)]
for ish in range(self.n_shells):
glist = [ GfReFreq(indices = inner, window = (om_min,om_max), n_points = n_om) for block,inner in gf_struct_parproj[ish] ]
G_loc.append(BlockGf(name_list = spn, block_list = glist, make_copies=False))
for ish in range(self.n_shells): G_loc[ish].zero()
glist = [GfReFreq(indices=inner, window=(om_min, om_max), n_points=n_om)
for block, inner in gf_struct_parproj[ish]]
G_loc.append(
BlockGf(name_list=spn, block_list=glist, make_copies=False))
for ish in range(self.n_shells):
G_loc[ish].zero()
DOS = { sp: numpy.zeros([n_om],numpy.float_) for sp in self.spin_block_names[self.SO] }
DOSproj = [ {} for ish in range(self.n_shells) ]
DOSproj_orb = [ {} for ish in range(self.n_shells) ]
DOS = {sp: numpy.zeros([n_om], numpy.float_)
for sp in self.spin_block_names[self.SO]}
DOSproj = [{} for ish in range(self.n_shells)]
DOSproj_orb = [{} for ish in range(self.n_shells)]
for ish in range(self.n_shells):
for sp in self.spin_block_names[self.SO]:
dim = self.shells[ish]['dim']
DOSproj[ish][sp] = numpy.zeros([n_om],numpy.float_)
DOSproj_orb[ish][sp] = numpy.zeros([n_om,dim,dim],numpy.float_)
DOSproj[ish][sp] = numpy.zeros([n_om], numpy.float_)
DOSproj_orb[ish][sp] = numpy.zeros(
[n_om, dim, dim], numpy.complex_)
ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(ik=ik,mu=mu,iw_or_w="w",broadening=broadening,mesh=mesh,with_Sigma=with_Sigma,with_dc=with_dc)
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_w *= self.bz_weights[ik]
# Non-projected DOS
for iom in range(n_om):
for bname,gf in G_latt_w:
DOS[bname][iom] -= gf.data[iom,:,:].imag.trace()/numpy.pi
for bname, gf in G_latt_w:
DOS[bname][iom] -= gf.data[iom, :, :].imag.trace() / \
numpy.pi
# Projected DOS:
for ish in range(self.n_shells):
tmp = G_loc[ish].copy()
for ir in range(self.n_parproj[ish]):
for bname,gf in tmp: tmp[bname] << self.downfold(ik,ish,bname,G_latt_w[bname],gf,shells='all',ir=ir)
for bname, gf in tmp:
tmp[bname] << self.downfold(ik, ish, bname, G_latt_w[
bname], gf, shells='all', ir=ir)
G_loc[ish] += tmp
# Collect data from mpi:
for bname in DOS:
DOS[bname] = mpi.all_reduce(mpi.world, DOS[bname], lambda x,y : x+y)
DOS[bname] = mpi.all_reduce(
mpi.world, DOS[bname], lambda x, y: x + y)
for ish in range(self.n_shells):
G_loc[ish] << mpi.all_reduce(mpi.world, G_loc[ish], lambda x,y : x+y)
G_loc[ish] << mpi.all_reduce(
mpi.world, G_loc[ish], lambda x, y: x + y)
mpi.barrier()
# Symmetrize and rotate to local coord. system if needed:
if self.symm_op != 0: G_loc = self.symmpar.symmetrize(G_loc)
if self.symm_op != 0:
G_loc = self.symmpar.symmetrize(G_loc)
if self.use_rotations:
for ish in range(self.n_shells):
for bname,gf in G_loc[ish]: G_loc[ish][bname] << self.rotloc(ish,gf,direction='toLocal',shells='all')
for bname, gf in G_loc[ish]:
G_loc[ish][bname] << self.rotloc(
ish, gf, direction='toLocal', shells='all')
# G_loc can now also be used to look at orbitally-resolved quantities
for ish in range(self.n_shells):
for bname,gf in G_loc[ish]:
for iom in range(n_om): DOSproj[ish][bname][iom] -= gf.data[iom,:,:].imag.trace()/numpy.pi
DOSproj_orb[ish][bname][:,:,:] -= gf.data[:,:,:].imag/numpy.pi
for bname, gf in G_loc[ish]:
for iom in range(n_om):
DOSproj[ish][bname][iom] -= gf.data[iom,
:, :].imag.trace() / numpy.pi
DOSproj_orb[ish][bname][
:, :, :] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:,:,:]
# Write to files
if save_to_file and mpi.is_master_node():
for sp in self.spin_block_names[self.SO]:
f = open('DOS_parproj_%s.dat'%sp, 'w')
for iom in range(n_om): f.write("%s %s\n"%(om_mesh[iom],DOS[sp][iom]))
f = open('DOS_parproj_%s.dat' % sp, 'w')
for iom in range(n_om):
f.write("%s %s\n" % (om_mesh[iom], DOS[sp][iom]))
f.close()
# Partial
for ish in range(self.n_shells):
f = open('DOS_parproj_%s_proj%s.dat'%(sp,ish),'w')
for iom in range(n_om): f.write("%s %s\n"%(om_mesh[iom],DOSproj[ish][sp][iom]))
f = open('DOS_parproj_%s_proj%s.dat' % (sp, ish), 'w')
for iom in range(n_om):
f.write("%s %s\n" %
(om_mesh[iom], DOSproj[ish][sp][iom]))
f.close()
# Orbitally-resolved
for i in range(self.shells[ish]['dim']):
for j in range(i,self.shells[ish]['dim']):
f = open('DOS_parproj_'+sp+'_proj'+str(ish)+'_'+str(i)+'_'+str(j)+'.dat','w')
for iom in range(n_om): f.write("%s %s\n"%(om_mesh[iom],DOSproj_orb[ish][sp][iom,i,j]))
for j in range(i, self.shells[ish]['dim']):
f = open('DOS_parproj_' + sp + '_proj' + str(ish) +
'_' + str(i) + '_' + str(j) + '.dat', 'w')
for iom in range(n_om):
f.write("%s %s %s\n" % (
om_mesh[iom], DOSproj_orb[ish][sp][iom, i, j].real,DOSproj_orb[ish][sp][iom, i, j].imag))
f.close()
return DOS, DOSproj, DOSproj_orb
# Uses .data of only GfReFreq objects.
def spaghettis(self,broadening=None,plot_shift=0.0,plot_range=None,ishell=None,mu=None,save_to_file='Akw_'):
def spaghettis(self, broadening=None, plot_shift=0.0, plot_range=None, ishell=None, mu=None, save_to_file='Akw_'):
"""
Calculates the correlated band structure using a real-frequency self energy.
@ -318,104 +364,131 @@ class SumkDFTTools(SumkDFT):
Data as it is also written to the files.
"""
assert hasattr(
self, "Sigma_imp_w"), "spaghettis: Set Sigma_imp_w first."
things_to_read = ['n_k', 'n_orbitals', 'proj_mat',
'hopping', 'n_parproj', 'proj_mat_all']
value_read = self.read_input_from_hdf(
subgrp=self.bands_data, things_to_read=things_to_read)
if not value_read:
return value_read
if ishell is not None:
things_to_read = ['rot_mat_all', 'rot_mat_all_time_inv']
value_read = self.read_input_from_hdf(
subgrp=self.parproj_data, things_to_read=things_to_read)
if not value_read:
return value_read
assert hasattr(self,"Sigma_imp_w"), "spaghettis: Set Sigma_imp_w first."
things_to_read = ['n_k','n_orbitals','proj_mat','hopping','n_parproj','proj_mat_all']
value_read = self.read_input_from_hdf(subgrp=self.bands_data,things_to_read=things_to_read)
if not value_read: return value_read
things_to_read = ['rot_mat_all','rot_mat_all_time_inv']
value_read = self.read_input_from_hdf(subgrp=self.parproj_data,things_to_read = things_to_read)
if not value_read: return value_read
if mu is None: mu = self.chemical_potential
if mu is None:
mu = self.chemical_potential
spn = self.spin_block_names[self.SO]
mesh = [x.real for x in self.Sigma_imp_w[0].mesh]
n_om = len(mesh)
if plot_range is None:
om_minplot = mesh[0] - 0.001
om_maxplot = mesh[n_om-1] + 0.001
om_maxplot = mesh[n_om - 1] + 0.001
else:
om_minplot = plot_range[0]
om_maxplot = plot_range[1]
if ishell is None:
Akw = { sp: numpy.zeros([self.n_k,n_om],numpy.float_) for sp in spn }
Akw = {sp: numpy.zeros([self.n_k, n_om], numpy.float_)
for sp in spn}
else:
Akw = { sp: numpy.zeros([self.shells[ishell]['dim'],self.n_k,n_om],numpy.float_) for sp in spn }
Akw = {sp: numpy.zeros(
[self.shells[ishell]['dim'], self.n_k, n_om], numpy.float_) for sp in spn}
if not ishell is None:
gf_struct_parproj = [ (sp, range(self.shells[ishell]['dim'])) for sp in spn ]
G_loc = BlockGf(name_block_generator = [ (block,GfReFreq(indices = inner, mesh = self.Sigma_imp_w[0].mesh))
for block,inner in gf_struct_parproj ], make_copies = False)
gf_struct_parproj = [
(sp, range(self.shells[ishell]['dim'])) for sp in spn]
G_loc = BlockGf(name_block_generator=[(block, GfReFreq(indices=inner, mesh=self.Sigma_imp_w[0].mesh))
for block, inner in gf_struct_parproj], make_copies=False)
G_loc.zero()
ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(ik=ik,mu=mu,iw_or_w="w",broadening=broadening)
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening)
if ishell is None:
# Non-projected A(k,w)
for iom in range(n_om):
if (mesh[iom] > om_minplot) and (mesh[iom] < om_maxplot):
for bname,gf in G_latt_w: Akw[bname][ik,iom] += gf.data[iom,:,:].imag.trace()/(-1.0*numpy.pi)
Akw[bname][ik,iom] += ik*plot_shift # shift Akw for plotting stacked k-resolved eps(k) curves
for bname, gf in G_latt_w:
Akw[bname][ik, iom] += gf.data[iom, :,
:].imag.trace() / (-1.0 * numpy.pi)
# shift Akw for plotting stacked k-resolved eps(k)
# curves
Akw[bname][ik, iom] += ik * plot_shift
else: # ishell not None
# Projected A(k,w):
G_loc.zero()
tmp = G_loc.copy()
for ir in range(self.n_parproj[ishell]):
for bname,gf in tmp: tmp[bname] << self.downfold(ik,ishell,bname,G_latt_w[bname],gf,shells='all',ir=ir)
for bname, gf in tmp:
tmp[bname] << self.downfold(ik, ishell, bname, G_latt_w[
bname], gf, shells='all', ir=ir)
G_loc += tmp
# Rotate to local frame
if self.use_rotations:
for bname,gf in G_loc: G_loc[bname] << self.rotloc(ishell,gf,direction='toLocal',shells='all')
for bname, gf in G_loc:
G_loc[bname] << self.rotloc(
ishell, gf, direction='toLocal', shells='all')
for iom in range(n_om):
if (mesh[iom] > om_minplot) and (mesh[iom] < om_maxplot):
for ish in range(self.shells[ishell]['dim']):
for sp in spn:
Akw[sp][ish,ik,iom] = G_loc[sp].data[iom,ish,ish].imag/(-1.0*numpy.pi)
Akw[sp][ish, ik, iom] = G_loc[sp].data[
iom, ish, ish].imag / (-1.0 * numpy.pi)
# Collect data from mpi
for sp in spn:
Akw[sp] = mpi.all_reduce(mpi.world, Akw[sp], lambda x,y : x+y)
Akw[sp] = mpi.all_reduce(mpi.world, Akw[sp], lambda x, y: x + y)
mpi.barrier()
if save_to_file and mpi.is_master_node():
if ishell is None:
for sp in spn: # loop over GF blocs:
f = open(save_to_file+sp+'.dat','w') # Open file for storage:
# Open file for storage:
f = open(save_to_file + sp + '.dat', 'w')
for ik in range(self.n_k):
for iom in range(n_om):
if (mesh[iom] > om_minplot) and (mesh[iom] < om_maxplot):
if plot_shift > 0.0001:
f.write('%s %s\n'%(mesh[iom],Akw[sp][ik,iom]))
f.write('%s %s\n' %
(mesh[iom], Akw[sp][ik, iom]))
else:
f.write('%s %s %s\n'%(ik,mesh[iom],Akw[sp][ik,iom]))
f.write('%s %s %s\n' %
(ik, mesh[iom], Akw[sp][ik, iom]))
f.write('\n')
f.close()
else: # ishell is not None
for sp in spn:
for ish in range(self.shells[ishell]['dim']):
f = open(save_to_file+str(ishell)+'_'+sp+'_proj'+str(ish)+'.dat','w') # Open file for storage:
# Open file for storage:
f = open(save_to_file + str(ishell) + '_' +
sp + '_proj' + str(ish) + '.dat', 'w')
for ik in range(self.n_k):
for iom in range(n_om):
if (mesh[iom] > om_minplot) and (mesh[iom] < om_maxplot):
if plot_shift > 0.0001:
f.write('%s %s\n'%(mesh[iom],Akw[sp][ish,ik,iom]))
f.write('%s %s\n' % (
mesh[iom], Akw[sp][ish, ik, iom]))
else:
f.write('%s %s %s\n'%(ik,mesh[iom],Akw[sp][ish,ik,iom]))
f.write('%s %s %s\n' % (
ik, mesh[iom], Akw[sp][ish, ik, iom]))
f.write('\n')
f.close()
return Akw
def partial_charges(self,beta=40,mu=None,with_Sigma=True,with_dc=True):
def partial_charges(self, beta=40, mu=None, with_Sigma=True, with_dc=True):
"""
Calculates the orbitally-resolved density matrix for all the orbitals considered in the input, consistent with
the definition of Wien2k. Hence, (possibly non-orthonormal) projectors have to be provided in the partial projectors subgroup of
@ -439,89 +512,103 @@ class SumkDFTTools(SumkDFT):
A list of density matrices projected to all shells provided in the input.
"""
things_to_read = ['dens_mat_below','n_parproj','proj_mat_all','rot_mat_all','rot_mat_all_time_inv']
value_read = self.read_input_from_hdf(subgrp=self.parproj_data,things_to_read = things_to_read)
if not value_read: return value_read
if self.symm_op: self.symmpar = Symmetry(self.hdf_file,subgroup=self.symmpar_data)
things_to_read = ['dens_mat_below', 'n_parproj',
'proj_mat_all', 'rot_mat_all', 'rot_mat_all_time_inv']
value_read = self.read_input_from_hdf(
subgrp=self.parproj_data, things_to_read=things_to_read)
if not value_read:
return value_read
if self.symm_op:
self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data)
spn = self.spin_block_names[self.SO]
ntoi = self.spin_names_to_ind[self.SO]
# Density matrix in the window
self.dens_mat_window = [ [ numpy.zeros([self.shells[ish]['dim'],self.shells[ish]['dim']],numpy.complex_)
for ish in range(self.n_shells) ]
for isp in range(len(spn)) ]
self.dens_mat_window = [[numpy.zeros([self.shells[ish]['dim'], self.shells[ish]['dim']], numpy.complex_)
for ish in range(self.n_shells)]
for isp in range(len(spn))]
# Set up G_loc
gf_struct_parproj = [ [ (sp, range(self.shells[ish]['dim'])) for sp in spn ]
for ish in range(self.n_shells) ]
gf_struct_parproj = [[(sp, range(self.shells[ish]['dim'])) for sp in spn]
for ish in range(self.n_shells)]
if with_Sigma:
G_loc = [ BlockGf(name_block_generator = [ (block,GfImFreq(indices = inner, mesh = self.Sigma_imp_iw[0].mesh))
for block,inner in gf_struct_parproj[ish] ], make_copies = False)
G_loc = [BlockGf(name_block_generator=[(block, GfImFreq(indices=inner, mesh=self.Sigma_imp_iw[0].mesh))
for block, inner in gf_struct_parproj[ish]], make_copies=False)
for ish in range(self.n_shells)]
beta = self.Sigma_imp_iw[0].mesh.beta
else:
G_loc = [ BlockGf(name_block_generator = [ (block,GfImFreq(indices = inner, beta = beta))
for block,inner in gf_struct_parproj[ish] ], make_copies = False)
G_loc = [BlockGf(name_block_generator=[(block, GfImFreq(indices=inner, beta=beta))
for block, inner in gf_struct_parproj[ish]], make_copies=False)
for ish in range(self.n_shells)]
for ish in range(self.n_shells): G_loc[ish].zero()
for ish in range(self.n_shells):
G_loc[ish].zero()
ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray):
G_latt_iw = self.lattice_gf(ik=ik,mu=mu,iw_or_w="iw",beta=beta,with_Sigma=with_Sigma,with_dc=with_dc)
G_latt_iw = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="iw", beta=beta, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_iw *= self.bz_weights[ik]
for ish in range(self.n_shells):
tmp = G_loc[ish].copy()
for ir in range(self.n_parproj[ish]):
for bname,gf in tmp: tmp[bname] << self.downfold(ik,ish,bname,G_latt_iw[bname],gf,shells='all',ir=ir)
for bname, gf in tmp:
tmp[bname] << self.downfold(ik, ish, bname, G_latt_iw[
bname], gf, shells='all', ir=ir)
G_loc[ish] += tmp
# Collect data from mpi:
for ish in range(self.n_shells):
G_loc[ish] << mpi.all_reduce(mpi.world, G_loc[ish], lambda x,y : x+y)
G_loc[ish] << mpi.all_reduce(
mpi.world, G_loc[ish], lambda x, y: x + y)
mpi.barrier()
# Symmetrize and rotate to local coord. system if needed:
if self.symm_op != 0: G_loc = self.symmpar.symmetrize(G_loc)
if self.symm_op != 0:
G_loc = self.symmpar.symmetrize(G_loc)
if self.use_rotations:
for ish in range(self.n_shells):
for bname,gf in G_loc[ish]: G_loc[ish][bname] << self.rotloc(ish,gf,direction='toLocal',shells='all')
for bname, gf in G_loc[ish]:
G_loc[ish][bname] << self.rotloc(
ish, gf, direction='toLocal', shells='all')
for ish in range(self.n_shells):
isp = 0
for bname,gf in G_loc[ish]:
for bname, gf in G_loc[ish]:
self.dens_mat_window[isp][ish] = G_loc[ish].density()[bname]
isp += 1
# Add density matrices to get the total:
dens_mat = [ [ self.dens_mat_below[ntoi[spn[isp]]][ish] + self.dens_mat_window[isp][ish]
for ish in range(self.n_shells) ]
for isp in range(len(spn)) ]
dens_mat = [[self.dens_mat_below[ntoi[spn[isp]]][ish] + self.dens_mat_window[isp][ish]
for ish in range(self.n_shells)]
for isp in range(len(spn))]
return dens_mat
def print_hamiltonian(self):
"""
Prints the Kohn-Sham Hamiltonian to the text files hamup.dat and hamdn.dat (no spin orbit-coupling), or to ham.dat (with spin-orbit coupling).
"""
if self.SP == 1 and self.SO == 0:
f1 = open('hamup.dat','w')
f2 = open('hamdn.dat','w')
f1 = open('hamup.dat', 'w')
f2 = open('hamdn.dat', 'w')
for ik in range(self.n_k):
for i in range(self.n_orbitals[ik,0]):
f1.write('%s %s\n'%(ik,self.hopping[ik,0,i,i].real))
for i in range(self.n_orbitals[ik,1]):
f2.write('%s %s\n'%(ik,self.hopping[ik,1,i,i].real))
for i in range(self.n_orbitals[ik, 0]):
f1.write('%s %s\n' %
(ik, self.hopping[ik, 0, i, i].real))
for i in range(self.n_orbitals[ik, 1]):
f2.write('%s %s\n' %
(ik, self.hopping[ik, 1, i, i].real))
f1.write('\n')
f2.write('\n')
f1.close()
f2.close()
else:
f = open('ham.dat','w')
f = open('ham.dat', 'w')
for ik in range(self.n_k):
for i in range(self.n_orbitals[ik,0]):
f.write('%s %s\n'%(ik,self.hopping[ik,0,i,i].real))
for i in range(self.n_orbitals[ik, 0]):
f.write('%s %s\n' %
(ik, self.hopping[ik, 0, i, i].real))
f.write('\n')
f.close()
@ -532,11 +619,13 @@ class SumkDFTTools(SumkDFT):
r"""
Reads the data for transport calculations from the hdf5 archive.
"""
thingstoread = ['band_window_optics','velocities_k']
self.read_input_from_hdf(subgrp=self.transp_data,things_to_read = thingstoread)
thingstoread = ['band_window','lattice_angles','lattice_constants','lattice_type','n_symmetries','rot_symmetries']
self.read_input_from_hdf(subgrp=self.misc_data,things_to_read = thingstoread)
thingstoread = ['band_window_optics', 'velocities_k']
self.read_input_from_hdf(
subgrp=self.transp_data, things_to_read=thingstoread)
thingstoread = ['band_window', 'lattice_angles', 'lattice_constants',
'lattice_type', 'n_symmetries', 'rot_symmetries']
self.read_input_from_hdf(
subgrp=self.misc_data, things_to_read=thingstoread)
def cellvolume(self, lattice_type, lattice_constants, latticeangle):
r"""
@ -565,14 +654,16 @@ class SumkDFTTools(SumkDFT):
c_al = numpy.cos(latticeangle[0])
c_be = numpy.cos(latticeangle[1])
c_ga = numpy.cos(latticeangle[2])
vol_c = a * b * c * numpy.sqrt(1 + 2 * c_al * c_be * c_ga - c_al ** 2 - c_be ** 2 - c_ga ** 2)
vol_c = a * b * c * \
numpy.sqrt(1 + 2 * c_al * c_be * c_ga -
c_al ** 2 - c_be ** 2 - c_ga ** 2)
det = {"P":1, "F":4, "B":2, "R":3, "H":1, "CXY":2, "CYZ":2, "CXZ":2}
det = {"P": 1, "F": 4, "B": 2, "R": 3,
"H": 1, "CXY": 2, "CYZ": 2, "CXZ": 2}
vol_p = vol_c / det[lattice_type]
return vol_c, vol_p
# Uses .data of only GfReFreq objects.
def transport_distribution(self, beta, directions=['xx'], energy_window=None, Om_mesh=[0.0], with_Sigma=False, n_om=None, broadening=0.0):
r"""
@ -607,39 +698,51 @@ class SumkDFTTools(SumkDFT):
Lorentzian broadening. It is necessary to specify the boradening if with_Sigma = False, otherwise this parameter can be set to 0.0.
"""
# Check if wien converter was called and read transport subgroup form hdf file
# Check if wien converter was called and read transport subgroup form
# hdf file
if mpi.is_master_node():
ar = HDFArchive(self.hdf_file, 'r')
if not (self.transp_data in ar): raise IOError, "transport_distribution: No %s subgroup in hdf file found! Call convert_transp_input first." %self.transp_data
if not (self.transp_data in ar):
raise IOError, "transport_distribution: No %s subgroup in hdf file found! Call convert_transp_input first." % self.transp_data
# check if outputs file was converted
if not ('n_symmetries' in ar['dft_misc_input']):
raise IOError, "transport_distribution: n_symmetries missing. Check if case.outputs file is present and call convert_misc_input() or convert_dft_input()."
self.read_transport_input_from_hdf()
if mpi.is_master_node():
# k-dependent-projections.
assert self.k_dep_projection == 1, "transport_distribution: k dependent projection is not implemented!"
# positive Om_mesh
assert all(Om >= 0.0 for Om in Om_mesh), "transport_distribution: Om_mesh should not contain negative values!"
assert all(
Om >= 0.0 for Om in Om_mesh), "transport_distribution: Om_mesh should not contain negative values!"
# Check if energy_window is sufficiently large and correct
if (energy_window[0] >= energy_window[1] or energy_window[0] >= 0 or energy_window[1] <= 0):
assert 0, "transport_distribution: energy_window wrong!"
if (abs(self.fermi_dis(energy_window[0],beta)*self.fermi_dis(-energy_window[0],beta)) > 1e-5
or abs(self.fermi_dis(energy_window[1],beta)*self.fermi_dis(-energy_window[1],beta)) > 1e-5):
mpi.report("\n####################################################################")
mpi.report("transport_distribution: WARNING - energy window might be too narrow!")
mpi.report("####################################################################\n")
if (abs(self.fermi_dis(energy_window[0], beta) * self.fermi_dis(-energy_window[0], beta)) > 1e-5
or abs(self.fermi_dis(energy_window[1], beta) * self.fermi_dis(-energy_window[1], beta)) > 1e-5):
mpi.report(
"\n####################################################################")
mpi.report(
"transport_distribution: WARNING - energy window might be too narrow!")
mpi.report(
"####################################################################\n")
n_inequiv_spin_blocks = self.SP + 1 - self.SO # up and down are equivalent if SP = 0
# up and down are equivalent if SP = 0
n_inequiv_spin_blocks = self.SP + 1 - self.SO
self.directions = directions
dir_to_int = {'x':0, 'y':1, 'z':2}
dir_to_int = {'x': 0, 'y': 1, 'z': 2}
# calculate A(k,w)
#######################################
# Define mesh for Green's function and in the specified energy window
if (with_Sigma == True):
self.omega = numpy.array([round(x.real,12) for x in self.Sigma_imp_w[0].mesh])
self.omega = numpy.array([round(x.real, 12)
for x in self.Sigma_imp_w[0].mesh])
mesh = None
mu = self.chemical_potential
n_om = len(self.omega)
@ -647,8 +750,10 @@ class SumkDFTTools(SumkDFT):
if energy_window is not None:
# Find according window in Sigma mesh
ioffset = numpy.sum(self.omega < energy_window[0]-max(Om_mesh))
self.omega = self.omega[numpy.logical_and(self.omega >= energy_window[0]-max(Om_mesh), self.omega <= energy_window[1]+max(Om_mesh))]
ioffset = numpy.sum(
self.omega < energy_window[0] - max(Om_mesh))
self.omega = self.omega[numpy.logical_and(self.omega >= energy_window[
0] - max(Om_mesh), self.omega <= energy_window[1] + max(Om_mesh))]
n_om = len(self.omega)
# Truncate Sigma to given omega window
@ -657,55 +762,69 @@ class SumkDFTTools(SumkDFT):
for icrsh in range(self.n_corr_shells):
Sigma_save = self.Sigma_imp_w[icrsh].copy()
spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
glist = lambda : [ GfReFreq(indices = inner, window=(self.omega[0], self.omega[-1]),n_points=n_om) for block, inner in self.gf_struct_sumk[icrsh]]
self.Sigma_imp_w[icrsh] = BlockGf(name_list = spn, block_list = glist(),make_copies=False)
for i,g in self.Sigma_imp_w[icrsh]:
glist = lambda: [GfReFreq(indices=inner, window=(self.omega[
0], self.omega[-1]), n_points=n_om) for block, inner in self.gf_struct_sumk[icrsh]]
self.Sigma_imp_w[icrsh] = BlockGf(
name_list=spn, block_list=glist(), make_copies=False)
for i, g in self.Sigma_imp_w[icrsh]:
for iL in g.indices:
for iR in g.indices:
for iom in xrange(n_om):
g.data[iom,iL,iR] = Sigma_save[i].data[ioffset+iom,iL,iR]
g.data[iom, iL, iR] = Sigma_save[
i].data[ioffset + iom, iL, iR]
else:
assert n_om is not None, "transport_distribution: Number of omega points (n_om) needed to calculate transport distribution!"
assert energy_window is not None, "transport_distribution: Energy window needed to calculate transport distribution!"
assert broadening != 0.0 and broadening is not None, "transport_distribution: Broadening necessary to calculate transport distribution!"
self.omega = numpy.linspace(energy_window[0]-max(Om_mesh),energy_window[1]+max(Om_mesh),n_om)
mesh = [energy_window[0]-max(Om_mesh), energy_window[1]+max(Om_mesh), n_om]
self.omega = numpy.linspace(
energy_window[0] - max(Om_mesh), energy_window[1] + max(Om_mesh), n_om)
mesh = [energy_window[0] -
max(Om_mesh), energy_window[1] + max(Om_mesh), n_om]
mu = 0.0
# Define mesh for optic conductivity
d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
iOm_mesh = numpy.array([round((Om / d_omega),0) for Om in Om_mesh])
iOm_mesh = numpy.array([round((Om / d_omega), 0) for Om in Om_mesh])
self.Om_mesh = iOm_mesh * d_omega
if mpi.is_master_node():
print "Chemical potential: ", mu
print "Using n_om = %s points in the energy_window [%s,%s]"%(n_om, self.omega[0], self.omega[-1]),
print "Using n_om = %s points in the energy_window [%s,%s]" % (n_om, self.omega[0], self.omega[-1]),
print "where the omega vector is:"
print self.omega
print "Calculation requested for Omega mesh: ", numpy.array(Om_mesh)
print "Omega mesh automatically repined to: ", self.Om_mesh
self.Gamma_w = {direction: numpy.zeros((len(self.Om_mesh), n_om), dtype=numpy.float_) for direction in self.directions}
self.Gamma_w = {direction: numpy.zeros(
(len(self.Om_mesh), n_om), dtype=numpy.float_) for direction in self.directions}
# Sum over all k-points
ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray):
# Calculate G_w for ik and initialize A_kw
G_w = self.lattice_gf(ik, mu, iw_or_w="w", beta=beta, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma)
G_w = self.lattice_gf(ik, mu, iw_or_w="w", beta=beta,
broadening=broadening, mesh=mesh, with_Sigma=with_Sigma)
A_kw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_)
for isp in range(n_inequiv_spin_blocks)]
for isp in range(n_inequiv_spin_blocks):
# copy data from G_w (swapaxes is used to have omega in the 3rd dimension)
A_kw[isp] = copy.deepcopy(G_w[self.spin_block_names[self.SO][isp]].data.swapaxes(0,1).swapaxes(1,2));
# copy data from G_w (swapaxes is used to have omega in the 3rd
# dimension)
A_kw[isp] = copy.deepcopy(G_w[self.spin_block_names[self.SO][
isp]].data.swapaxes(0, 1).swapaxes(1, 2))
# calculate A(k,w) for each frequency
for iw in xrange(n_om):
A_kw[isp][:,:,iw] = -1.0/(2.0*numpy.pi*1j)*(A_kw[isp][:,:,iw]-numpy.conjugate(numpy.transpose(A_kw[isp][:,:,iw])))
A_kw[isp][:, :, iw] = -1.0 / (2.0 * numpy.pi * 1j) * (
A_kw[isp][:, :, iw] - numpy.conjugate(numpy.transpose(A_kw[isp][:, :, iw])))
b_min = max(self.band_window[isp][ik, 0], self.band_window_optics[isp][ik, 0])
b_max = min(self.band_window[isp][ik, 1], self.band_window_optics[isp][ik, 1])
A_i = slice(b_min - self.band_window[isp][ik, 0], b_max - self.band_window[isp][ik, 0] + 1)
v_i = slice(b_min - self.band_window_optics[isp][ik, 0], b_max - self.band_window_optics[isp][ik, 0] + 1)
b_min = max(self.band_window[isp][
ik, 0], self.band_window_optics[isp][ik, 0])
b_max = min(self.band_window[isp][
ik, 1], self.band_window_optics[isp][ik, 1])
A_i = slice(
b_min - self.band_window[isp][ik, 0], b_max - self.band_window[isp][ik, 0] + 1)
v_i = slice(b_min - self.band_window_optics[isp][
ik, 0], b_max - self.band_window_optics[isp][ik, 0] + 1)
# loop over all symmetries
for R in self.rot_symmetries:
@ -713,27 +832,29 @@ class SumkDFTTools(SumkDFT):
vel_R = copy.deepcopy(self.velocities_k[isp][ik])
for nu1 in range(self.band_window_optics[isp][ik, 1] - self.band_window_optics[isp][ik, 0] + 1):
for nu2 in range(self.band_window_optics[isp][ik, 1] - self.band_window_optics[isp][ik, 0] + 1):
vel_R[nu1][nu2][:] = numpy.dot(R, vel_R[nu1][nu2][:])
vel_R[nu1][nu2][:] = numpy.dot(
R, vel_R[nu1][nu2][:])
# calculate Gamma_w for each direction from the velocities vel_R and the spectral function A_kw
# calculate Gamma_w for each direction from the velocities
# vel_R and the spectral function A_kw
for direction in self.directions:
for iw in xrange(n_om):
for iq in range(len(self.Om_mesh)):
if(iw + iOm_mesh[iq] >= n_om or self.omega[iw] < -self.Om_mesh[iq] + energy_window[0] or self.omega[iw] > self.Om_mesh[iq] + energy_window[1]): continue
if(iw + iOm_mesh[iq] >= n_om or self.omega[iw] < -self.Om_mesh[iq] + energy_window[0] or self.omega[iw] > self.Om_mesh[iq] + energy_window[1]):
continue
self.Gamma_w[direction][iq, iw] += (numpy.dot(numpy.dot(numpy.dot(vel_R[v_i, v_i, dir_to_int[direction[0]]],
A_kw[isp][A_i, A_i, iw + iOm_mesh[iq]]), vel_R[v_i, v_i, dir_to_int[direction[1]]]),
A_kw[isp][A_i, A_i, iw ]).trace().real * self.bz_weights[ik])
A_kw[isp][A_i, A_i, iw]).trace().real * self.bz_weights[ik])
for direction in self.directions:
self.Gamma_w[direction] = (mpi.all_reduce(mpi.world, self.Gamma_w[direction], lambda x, y : x + y)
self.Gamma_w[direction] = (mpi.all_reduce(mpi.world, self.Gamma_w[direction], lambda x, y: x + y)
/ self.cellvolume(self.lattice_type, self.lattice_constants, self.lattice_angles)[1] / self.n_symmetries)
def transport_coefficient(self, direction, iq, n, beta, method=None):
r"""
Calculates the transport coefficient A_n in a given direction for a given :math:`\Omega`. The required members (Gamma_w, directions, Om_mesh) have to be obtained first
by calling the function :meth:`transport_distribution <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`. For n>0 A is set to NaN if :math:`\Omega` is not 0.0.
by calling the function :meth:`transport_distribution <dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`. For n>0 A is set to NaN if :math:`\Omega` is not 0.0.
Parameters
----------
@ -755,47 +876,51 @@ class SumkDFTTools(SumkDFT):
Transport coefficient.
"""
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
assert hasattr(self,'Gamma_w'), "transport_coefficient: Run transport_distribution first or load data from h5!"
assert hasattr(
self, 'Gamma_w'), "transport_coefficient: Run transport_distribution first or load data from h5!"
if (self.Om_mesh[iq] == 0.0 or n == 0.0):
A = 0.0
# setup the integrand
if (self.Om_mesh[iq] == 0.0):
A_int = self.Gamma_w[direction][iq] * (self.fermi_dis(self.omega,beta) * self.fermi_dis(-self.omega,beta)) * (self.omega*beta)**n
A_int = self.Gamma_w[direction][iq] * (self.fermi_dis(
self.omega, beta) * self.fermi_dis(-self.omega, beta)) * (self.omega * beta)**n
elif (n == 0.0):
A_int = self.Gamma_w[direction][iq] * (self.fermi_dis(self.omega,beta) - self.fermi_dis(self.omega+self.Om_mesh[iq],beta))/(self.Om_mesh[iq]*beta)
A_int = self.Gamma_w[direction][iq] * (self.fermi_dis(self.omega, beta) - self.fermi_dis(
self.omega + self.Om_mesh[iq], beta)) / (self.Om_mesh[iq] * beta)
# w-integration
if method == 'quad':
# quad on interpolated w-points with cubic spline
A_int_interp = interp1d(self.omega,A_int,kind='cubic')
A = quad(A_int_interp, min(self.omega), max(self.omega), epsabs=1.0e-12,epsrel=1.0e-12,limit = 500)
A_int_interp = interp1d(self.omega, A_int, kind='cubic')
A = quad(A_int_interp, min(self.omega), max(self.omega),
epsabs=1.0e-12, epsrel=1.0e-12, limit=500)
A = A[0]
elif method == 'simps':
# simpson rule for w-grid
A = simps(A_int,self.omega)
A = simps(A_int, self.omega)
elif method == 'trapz':
# trapezoidal rule for w-grid
A = numpy.trapz(A_int,self.omega)
A = numpy.trapz(A_int, self.omega)
else:
# rectangular integration for w-grid (orignal implementation)
d_w = self.omega[1] - self.omega[0]
for iw in xrange(self.Gamma_w[direction].shape[1]):
A += A_int[iw]*d_w
A = A * numpy.pi * (2.0-self.SP)
A += A_int[iw] * d_w
A = A * numpy.pi * (2.0 - self.SP)
else:
A = numpy.nan
return A
def conductivity_and_seebeck(self, beta, method=None):
r"""
Calculates the Seebeck coefficient and the optical conductivity by calling
:meth:`transport_coefficient <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.transport_coefficient>`.
:meth:`transport_coefficient <dft.sumk_dft_tools.SumkDFTTools.transport_coefficient>`.
The required members (Gamma_w, directions, Om_mesh) have to be obtained first by calling the function
:meth:`transport_distribution <pytriqs.applications.dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`.
:meth:`transport_distribution <dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`.
Parameters
----------
@ -811,26 +936,36 @@ class SumkDFTTools(SumkDFT):
Seebeck coefficient in each direction. If zero is not present in Om_mesh the Seebeck coefficient is set to NaN.
"""
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
assert hasattr(self,'Gamma_w'), "conductivity_and_seebeck: Run transport_distribution first or load data from h5!"
assert hasattr(
self, 'Gamma_w'), "conductivity_and_seebeck: Run transport_distribution first or load data from h5!"
n_q = self.Gamma_w[self.directions[0]].shape[0]
A0 = {direction: numpy.full((n_q,),numpy.nan) for direction in self.directions}
A1 = {direction: numpy.full((n_q,),numpy.nan) for direction in self.directions}
A0 = {direction: numpy.full((n_q,), numpy.nan)
for direction in self.directions}
A1 = {direction: numpy.full((n_q,), numpy.nan)
for direction in self.directions}
self.seebeck = {direction: numpy.nan for direction in self.directions}
self.optic_cond = {direction: numpy.full((n_q,),numpy.nan) for direction in self.directions}
self.optic_cond = {direction: numpy.full(
(n_q,), numpy.nan) for direction in self.directions}
for direction in self.directions:
for iq in xrange(n_q):
A0[direction][iq] = self.transport_coefficient(direction, iq=iq, n=0, beta=beta, method=method)
A1[direction][iq] = self.transport_coefficient(direction, iq=iq, n=1, beta=beta, method=method)
A0[direction][iq] = self.transport_coefficient(
direction, iq=iq, n=0, beta=beta, method=method)
A1[direction][iq] = self.transport_coefficient(
direction, iq=iq, n=1, beta=beta, method=method)
print "A_0 in direction %s for Omega = %.2f %e a.u." % (direction, self.Om_mesh[iq], A0[direction][iq])
print "A_1 in direction %s for Omega = %.2f %e a.u." % (direction, self.Om_mesh[iq], A1[direction][iq])
if ~numpy.isnan(A1[direction][iq]):
# Seebeck is overwritten if there is more than one Omega = 0 in Om_mesh
self.seebeck[direction] = - A1[direction][iq] / A0[direction][iq] * 86.17
self.optic_cond[direction] = beta * A0[direction] * 10700.0 / numpy.pi
# Seebeck is overwritten if there is more than one Omega =
# 0 in Om_mesh
self.seebeck[direction] = - \
A1[direction][iq] / A0[direction][iq] * 86.17
self.optic_cond[direction] = beta * \
A0[direction] * 10700.0 / numpy.pi
for iq in xrange(n_q):
print "Conductivity in direction %s for Omega = %.2f %f x 10^4 Ohm^-1 cm^-1" % (direction, self.Om_mesh[iq], self.optic_cond[direction][iq])
if not (numpy.isnan(A1[direction][iq])):
@ -838,8 +973,7 @@ class SumkDFTTools(SumkDFT):
return self.optic_cond, self.seebeck
def fermi_dis(self,w,beta):
def fermi_dis(self, w, beta):
r"""
Fermi distribution.
@ -857,4 +991,4 @@ class SumkDFTTools(SumkDFT):
-------
f : double
"""
return 1.0/(numpy.exp(w*beta)+1)
return 1.0 / (numpy.exp(w * beta) + 1)

78
python/symmetry.py
View File

@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,14 +18,16 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
import copy,numpy
import copy
import numpy
from types import *
from pytriqs.gf.local import *
from pytriqs.archive import *
import pytriqs.utility.mpi as mpi
class Symmetry:
"""
This class provides the routines for applying symmetry operations for the k sums.
@ -33,7 +35,7 @@ class Symmetry:
rotational matrices for each symmetry operation.
"""
def __init__(self, hdf_file, subgroup = None):
def __init__(self, hdf_file, subgroup=None):
"""
Initialises the class.
@ -46,39 +48,44 @@ class Symmetry:
the data is stored at the root of the hdf5 archive.
"""
assert type(hdf_file) == StringType, "Symmetry: hdf_file must be a filename."
assert type(
hdf_file) == StringType, "Symmetry: hdf_file must be a filename."
self.hdf_file = hdf_file
things_to_read = ['n_symm','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
for it in things_to_read: setattr(self,it,0)
things_to_read = ['n_symm', 'n_atoms', 'perm',
'orbits', 'SO', 'SP', 'time_inv', 'mat', 'mat_tinv']
for it in things_to_read:
setattr(self, it, 0)
if mpi.is_master_node():
#Read the stuff on master:
ar = HDFArchive(hdf_file,'r')
# Read the stuff on master:
ar = HDFArchive(hdf_file, 'r')
if subgroup is None:
ar2 = ar
else:
ar2 = ar[subgroup]
for it in things_to_read: setattr(self,it,ar2[it])
for it in things_to_read:
setattr(self, it, ar2[it])
del ar2
del ar
# Broadcasting
for it in things_to_read: setattr(self,it,mpi.bcast(getattr(self,it)))
for it in things_to_read:
setattr(self, it, mpi.bcast(getattr(self, it)))
# now define the mapping of orbitals:
# self.orb_map[iorb] = jorb gives the permutation of the orbitals as given in the list, when the
# permutation of the atoms is done:
self.n_orbits = len(self.orbits)
self.orb_map = [ [0 for iorb in range(self.n_orbits)] for i_symm in range(self.n_symm) ]
self.orb_map = [[0 for iorb in range(
self.n_orbits)] for i_symm in range(self.n_symm)]
for i_symm in range(self.n_symm):
for iorb in range(self.n_orbits):
srch = copy.deepcopy(self.orbits[iorb])
srch['atom'] = self.perm[i_symm][self.orbits[iorb]['atom']-1]
srch['atom'] = self.perm[i_symm][self.orbits[iorb]['atom'] - 1]
self.orb_map[i_symm][iorb] = self.orbits.index(srch)
def symmetrize(self,obj):
def symmetrize(self, obj):
"""
Symmetrizes a given object.
@ -97,18 +104,24 @@ class Symmetry:
Symmetrized object, of the same type as input object.
"""
assert isinstance(obj,list), "symmetrize: obj has to be a list of objects."
assert len(obj) == self.n_orbits, "symmetrize: obj has to be a list of the same length as defined in the init."
assert isinstance(
obj, list), "symmetrize: obj has to be a list of objects."
assert len(
obj) == self.n_orbits, "symmetrize: obj has to be a list of the same length as defined in the init."
if isinstance(obj[0],BlockGf):
symm_obj = [ obj[i].copy() for i in range(len(obj)) ] # here the result is stored, it is a BlockGf!
for iorb in range(self.n_orbits): symm_obj[iorb].zero() # set to zero
if isinstance(obj[0], BlockGf):
# here the result is stored, it is a BlockGf!
symm_obj = [obj[i].copy() for i in range(len(obj))]
for iorb in range(self.n_orbits):
symm_obj[iorb].zero() # set to zero
else:
# if not a BlockGf, we assume it is a matrix (density matrix), has to be complex since self.mat is complex!
symm_obj = [ copy.deepcopy(obj[i]) for i in range(len(obj)) ]
# if not a BlockGf, we assume it is a matrix (density matrix), has
# to be complex since self.mat is complex!
symm_obj = [copy.deepcopy(obj[i]) for i in range(len(obj))]
for iorb in range(self.n_orbits):
if type(symm_obj[iorb]) == DictType:
for ii in symm_obj[iorb]: symm_obj[iorb][ii] *= 0.0
for ii in symm_obj[iorb]:
symm_obj[iorb][ii] *= 0.0
else:
symm_obj[iorb] *= 0.0
@ -118,12 +131,15 @@ class Symmetry:
dim = self.orbits[iorb]['dim']
jorb = self.orb_map[i_symm][iorb]
if isinstance(obj[0],BlockGf):
if isinstance(obj[0], BlockGf):
tmp = obj[iorb].copy()
if self.time_inv[i_symm]: tmp << tmp.transpose()
for bname,gf in tmp: tmp[bname].from_L_G_R(self.mat[i_symm][iorb],tmp[bname],self.mat[i_symm][iorb].conjugate().transpose())
tmp *= 1.0/self.n_symm
if self.time_inv[i_symm]:
tmp << tmp.transpose()
for bname, gf in tmp:
tmp[bname].from_L_G_R(self.mat[i_symm][iorb], tmp[bname], self.mat[
i_symm][iorb].conjugate().transpose())
tmp *= 1.0 / self.n_symm
symm_obj[jorb] += tmp
else:
@ -131,17 +147,17 @@ class Symmetry:
if type(obj[iorb]) == DictType:
for ii in obj[iorb]:
if self.time_inv[i_symm] == 0:
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb][ii]),
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[i_symm][iorb], obj[iorb][ii]),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
else:
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb][ii].conjugate()),
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[i_symm][iorb], obj[iorb][ii].conjugate()),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
else:
if self.time_inv[i_symm] == 0:
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb]),
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[i_symm][iorb], obj[iorb]),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
else:
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb].conjugate()),
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[i_symm][iorb], obj[iorb].conjugate()),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
# Markus: This does not what it is supposed to do, check how this should work (keep for now)

89
python/trans_basis.py
View File

@ -6,6 +6,7 @@ import pytriqs.utility.mpi as mpi
import numpy
import copy
class TransBasis:
"""
Computates rotations into a new basis, using the condition that a given property is diagonal in the new basis.
@ -35,19 +36,19 @@ class TransBasis:
mpi.report("trans_basis: give SK instance or HDF filename!")
return 0
Converter = Wien2kConverter(filename=hdf_datafile,repacking=False)
Converter = Wien2kConverter(filename=hdf_datafile, repacking=False)
Converter.convert_dft_input()
del Converter
self.SK = SumkDFT(hdf_file=hdf_datafile+'.h5',use_dft_blocks=False)
self.SK = SumkDFT(hdf_file=hdf_datafile +
'.h5', use_dft_blocks=False)
else:
self.SK = SK
self.T = copy.deepcopy(self.SK.T[0])
self.w = numpy.identity(SK.corr_shells[0]['dim'])
def calculate_diagonalisation_matrix(self, prop_to_be_diagonal = 'eal'):
def calculate_diagonalisation_matrix(self, prop_to_be_diagonal='eal'):
"""
Calculates the diagonalisation matrix w, and stores it as member of the class.
@ -69,26 +70,28 @@ class TransBasis:
if prop_to_be_diagonal == 'eal':
prop = self.SK.eff_atomic_levels()[0]
elif prop_to_be_diagonal == 'dm':
prop = self.SK.density_matrix(method = 'using_point_integration')[0]
prop = self.SK.density_matrix(method='using_point_integration')[0]
else:
mpi.report("trans_basis: not a valid quantitiy to be diagonal. Choices are 'eal' or 'dm'.")
mpi.report(
"trans_basis: not a valid quantitiy to be diagonal. Choices are 'eal' or 'dm'.")
return 0
if self.SK.SO == 0:
self.eig,self.w = numpy.linalg.eigh(prop['up'])
self.eig, self.w = numpy.linalg.eigh(prop['up'])
# calculate new Transformation matrix
self.T = numpy.dot(self.T.transpose().conjugate(),self.w).conjugate().transpose()
self.T = numpy.dot(self.T.transpose().conjugate(),
self.w).conjugate().transpose()
else:
self.eig,self.w = numpy.linalg.eigh(prop['ud'])
self.eig, self.w = numpy.linalg.eigh(prop['ud'])
# calculate new Transformation matrix
self.T = numpy.dot(self.T.transpose().conjugate(),self.w).conjugate().transpose()
self.T = numpy.dot(self.T.transpose().conjugate(),
self.w).conjugate().transpose()
# measure for the 'unity' of the transformation:
wsqr = sum(abs(self.w.diagonal())**2)/self.w.diagonal().size
wsqr = sum(abs(self.w.diagonal())**2) / self.w.diagonal().size
return wsqr
def rotate_gf(self,gf_to_rot):
def rotate_gf(self, gf_to_rot):
"""
Uses the diagonalisation matrix w to rotate a given GF into the new basis.
@ -104,29 +107,33 @@ class TransBasis:
"""
# build a full GF
gfrotated = BlockGf( name_block_generator = [ (block,GfImFreq(indices = inner, mesh = gf_to_rot.mesh)) for block,inner in self.SK.gf_struct_sumk[0] ], make_copies = False)
gfrotated = BlockGf(name_block_generator=[(block, GfImFreq(
indices=inner, mesh=gf_to_rot.mesh)) for block, inner in self.SK.gf_struct_sumk[0]], make_copies=False)
# transform the CTQMC blocks to the full matrix:
ish = self.SK.corr_to_inequiv[0] # ish is the index of the inequivalent shell corresponding to icrsh
# ish is the index of the inequivalent shell corresponding to icrsh
ish = self.SK.corr_to_inequiv[0]
for block, inner in self.gf_struct_solver[ish].iteritems():
for ind1 in inner:
for ind2 in inner:
gfrotated[self.SK.solver_to_sumk_block[ish][block]][ind1,ind2] << gf_to_rot[block][ind1,ind2]
gfrotated[self.SK.solver_to_sumk_block[ish][block]][
ind1, ind2] << gf_to_rot[block][ind1, ind2]
# Rotate using the matrix w
for bname,gf in gfrotated:
gfrotated[bname].from_L_G_R(self.w.transpose().conjugate(),gfrotated[bname],self.w)
for bname, gf in gfrotated:
gfrotated[bname].from_L_G_R(
self.w.transpose().conjugate(), gfrotated[bname], self.w)
gfreturn = gf_to_rot.copy()
# Put back into CTQMC basis:
for block, inner in self.gf_struct_solver[ish].iteritems():
for ind1 in inner:
for ind2 in inner:
gfreturn[block][ind1,ind2] << gfrotated[self.SK.solver_to_sumk_block[0][block]][ind1,ind2]
gfreturn[block][ind1, ind2] << gfrotated[
self.SK.solver_to_sumk_block[0][block]][ind1, ind2]
return gfreturn
def write_trans_file(self, filename):
"""
Writes the new transformation T into a file readable by dmftproj. By that, the requested quantity is
@ -138,7 +145,7 @@ class TransBasis:
Name of the file where the transformation is stored.
"""
f = open(filename,'w')
f = open(filename, 'w')
Tnew = self.T.conjugate()
dim = self.SK.corr_shells[0]['dim']
@ -147,43 +154,43 @@ class TransBasis:
for i in range(dim):
st = ''
for k in range(dim):
st += " %9.6f"%(Tnew[i,k].real)
st += " %9.6f"%(Tnew[i,k].imag)
for k in range(2*dim):
st += " %9.6f" % (Tnew[i, k].real)
st += " %9.6f" % (Tnew[i, k].imag)
for k in range(2 * dim):
st += " 0.0"
if i < (dim-1):
f.write("%s\n"%(st))
if i < (dim - 1):
f.write("%s\n" % (st))
else:
st1 = st.replace(' ','*',1)
f.write("%s\n"%(st1))
st1 = st.replace(' ', '*', 1)
f.write("%s\n" % (st1))
for i in range(dim):
st = ''
for k in range(2*dim):
for k in range(2 * dim):
st += " 0.0"
for k in range(dim):
st += " %9.6f"%(Tnew[i,k].real)
st += " %9.6f"%(Tnew[i,k].imag)
st += " %9.6f" % (Tnew[i, k].real)
st += " %9.6f" % (Tnew[i, k].imag)
if i < (dim-1):
f.write("%s\n"%(st))
if i < (dim - 1):
f.write("%s\n" % (st))
else:
st1 = st.replace(' ','*',1)
f.write("%s\n"%(st1))
st1 = st.replace(' ', '*', 1)
f.write("%s\n" % (st1))
else:
for i in range(dim):
st = ''
for k in range(dim):
st += " %9.6f"%(Tnew[i,k].real)
st += " %9.6f"%(Tnew[i,k].imag)
st += " %9.6f" % (Tnew[i, k].real)
st += " %9.6f" % (Tnew[i, k].imag)
if i < (dim-1):
f.write("%s\n"%(st))
if i < (dim - 1):
f.write("%s\n" % (st))
else:
st1 = st.replace(' ','*',1)
f.write("%s\n"%(st1))
st1 = st.replace(' ', '*', 1)
f.write("%s\n" % (st1))
f.close()

83
python/update_archive.py
View File

@ -15,13 +15,16 @@ Please keep a copy of your old archive as this script is
If you encounter any problem please report it on github!
"""
def convert_shells(shells):
shell_entries = ['atom', 'sort', 'l', 'dim']
return [ {name: int(val) for name, val in zip(shell_entries, shells[ish])} for ish in range(len(shells)) ]
return [{name: int(val) for name, val in zip(shell_entries, shells[ish])} for ish in range(len(shells))]
def convert_corr_shells(corr_shells):
corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
return [ {name: int(val) for name, val in zip(corr_shell_entries, corr_shells[icrsh])} for icrsh in range(len(corr_shells)) ]
return [{name: int(val) for name, val in zip(corr_shell_entries, corr_shells[icrsh])} for icrsh in range(len(corr_shells))]
def det_shell_equivalence(corr_shells):
corr_to_inequiv = [0 for i in range(len(corr_shells))]
@ -29,20 +32,20 @@ def det_shell_equivalence(corr_shells):
n_inequiv_shells = 1
if len(corr_shells) > 1:
inequiv_sort = [ corr_shells[0]['sort'] ]
inequiv_l = [ corr_shells[0]['l'] ]
for i in range(len(corr_shells)-1):
inequiv_sort = [corr_shells[0]['sort']]
inequiv_l = [corr_shells[0]['l']]
for i in range(len(corr_shells) - 1):
is_equiv = False
for j in range(n_inequiv_shells):
if (inequiv_sort[j]==corr_shells[i+1]['sort']) and (inequiv_l[j]==corr_shells[i+1]['l']):
if (inequiv_sort[j] == corr_shells[i + 1]['sort']) and (inequiv_l[j] == corr_shells[i + 1]['l']):
is_equiv = True
corr_to_inequiv[i+1] = j
if is_equiv==False:
corr_to_inequiv[i+1] = n_inequiv_shells
corr_to_inequiv[i + 1] = j
if is_equiv == False:
corr_to_inequiv[i + 1] = n_inequiv_shells
n_inequiv_shells += 1
inequiv_sort.append( corr_shells[i+1]['sort'] )
inequiv_l.append( corr_shells[i+1]['l'] )
inequiv_to_corr.append( i+1 )
inequiv_sort.append(corr_shells[i + 1]['sort'])
inequiv_l.append(corr_shells[i + 1]['l'])
inequiv_to_corr.append(i + 1)
return n_inequiv_shells, corr_to_inequiv, inequiv_to_corr
@ -57,41 +60,43 @@ else: # Assume updating an old v1.0 script
A = h5py.File(filename)
# Rename groups
old_to_new = {'SumK_LDA':'dft_input', 'SumK_LDA_ParProj':'dft_parproj_input',
'SymmCorr':'dft_symmcorr_input', 'SymmPar':'dft_symmpar_input', 'SumK_LDA_Bands':'dft_bands_input'}
old_to_new = {'SumK_LDA': 'dft_input', 'SumK_LDA_ParProj': 'dft_parproj_input',
'SymmCorr': 'dft_symmcorr_input', 'SymmPar': 'dft_symmpar_input', 'SumK_LDA_Bands': 'dft_bands_input'}
for old, new in old_to_new.iteritems():
if old not in A.keys(): continue
print "Changing %s to %s ..."%(old, new)
A.copy(old,new)
if old not in A.keys():
continue
print "Changing %s to %s ..." % (old, new)
A.copy(old, new)
del(A[old])
# Move output items from dft_input to user_data
move_to_output = ['chemical_potential','dc_imp','dc_energ']
move_to_output = ['chemical_potential', 'dc_imp', 'dc_energ']
for obj in move_to_output:
if obj in A['dft_input'].keys():
if 'user_data' not in A: A.create_group('user_data')
print "Moving %s to user_data ..."%obj
A.copy('dft_input/'+obj,'user_data/'+obj)
if 'user_data' not in A:
A.create_group('user_data')
print "Moving %s to user_data ..." % obj
A.copy('dft_input/' + obj, 'user_data/' + obj)
del(A['dft_input'][obj])
# Delete obsolete quantities
to_delete = ['gf_struct_solver','map_inv','map','deg_shells','h_field']
to_delete = ['gf_struct_solver', 'map_inv', 'map', 'deg_shells', 'h_field']
for obj in to_delete:
if obj in A['dft_input'].keys():
del(A['dft_input'][obj])
if from_v == 'v1.0':
# Update shells and corr_shells to list of dicts
shells_old = HDFArchive(filename,'r')['dft_input']['shells']
corr_shells_old = HDFArchive(filename,'r')['dft_input']['corr_shells']
shells_old = HDFArchive(filename, 'r')['dft_input']['shells']
corr_shells_old = HDFArchive(filename, 'r')['dft_input']['corr_shells']
shells = convert_shells(shells_old)
corr_shells = convert_corr_shells(corr_shells_old)
del(A['dft_input']['shells'])
del(A['dft_input']['corr_shells'])
A.close()
# Need to use HDFArchive for the following
HDFArchive(filename,'a')['dft_input']['shells'] = shells
HDFArchive(filename,'a')['dft_input']['corr_shells'] = corr_shells
HDFArchive(filename, 'a')['dft_input']['shells'] = shells
HDFArchive(filename, 'a')['dft_input']['corr_shells'] = corr_shells
A = h5py.File(filename)
# Add shell equivalency quantities
@ -102,32 +107,36 @@ if 'n_inequiv_shells' not in A['dft_input']:
A['dft_input']['inequiv_to_corr'] = equiv_shell_info[2]
# Rename variables
groups = ['dft_symmcorr_input','dft_symmpar_input']
groups = ['dft_symmcorr_input', 'dft_symmpar_input']
for group in groups:
if group not in A.keys(): continue
if 'n_s' not in A[group]: continue
if group not in A.keys():
continue
if 'n_s' not in A[group]:
continue
print "Changing n_s to n_symm ..."
A[group].move('n_s','n_symm')
A[group].move('n_s', 'n_symm')
# Convert orbits to list of dicts
orbits_old = HDFArchive(filename,'r')[group]['orbits']
orbits_old = HDFArchive(filename, 'r')[group]['orbits']
orbits = convert_corr_shells(orbits_old)
del(A[group]['orbits'])
A.close()
HDFArchive(filename,'a')[group]['orbits'] = orbits
HDFArchive(filename, 'a')[group]['orbits'] = orbits
A = h5py.File(filename)
groups = ['dft_parproj_input']
for group in groups:
if group not in A.keys(): continue
if 'proj_mat_pc' not in A[group]: continue
if group not in A.keys():
continue
if 'proj_mat_pc' not in A[group]:
continue
print "Changing proj_mat_pc to proj_mat_all ..."
A[group].move('proj_mat_pc','proj_mat_all')
A[group].move('proj_mat_pc', 'proj_mat_all')
A.close()
# Repack to reclaim disk space
retcode = subprocess.call(["h5repack","-i%s"%filename, "-otemphgfrt.h5"])
retcode = subprocess.call(["h5repack", "-i%s" % filename, "-otemphgfrt.h5"])
if retcode != 0:
print "h5repack failed!"
else:
subprocess.call(["mv","-f","temphgfrt.h5","%s"%filename])
subprocess.call(["mv", "-f", "temphgfrt.h5", "%s" % filename])

4
python/version.py.in
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@ -21,10 +21,10 @@
version = "@DFT_TOOLS_VERSION@"
triqs_hash = "@TRIQS_GIT_HASH@"
cthyb_hash = "@CTHYB_GIT_HASH@"
dft_tools_hash = "@DFT_TOOLS_GIT_HASH@"
def show_version():
print "\nYou are using the dft_tools version %s\n"%version
def show_git_hash():
print "\nYou are using the dft_tools git hash %s based on triqs git hash %s\n"%(cthyb_hash, triqs_hash)
print "\nYou are using the dft_tools git hash %s based on triqs git hash %s\n"%(dft_tools_hash, triqs_hash)

3
test/CMakeLists.txt
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@ -14,5 +14,8 @@ triqs_add_python_test(sumkdft_basic)
triqs_add_python_test(srvo3_Gloc)
triqs_add_python_test(srvo3_transp)
triqs_add_python_test(sigma_from_file)
triqs_add_python_test(blockstructure)
# VASP converter tests
add_subdirectory(plovasp)

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test/blockstructure.in.h5 Normal file
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83
test/blockstructure.py Normal file
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@ -0,0 +1,83 @@
from pytriqs.applications.dft.sumk_dft import *
from pytriqs.utility.h5diff import h5diff
from pytriqs.gf.local import *
from pytriqs.utility.comparison_tests import assert_block_gfs_are_close
from pytriqs.applications.dft import BlockStructure
SK = SumkDFT('blockstructure.in.h5',use_dft_blocks=True)
original_bs = SK.block_structure
# check pick_gf_struct_solver
pick1 = original_bs.copy()
pick1.pick_gf_struct_solver([{'up_0': [1], 'up_1': [0], 'down_1': [0]}])
# check loading a block_structure from file
SK.block_structure = SK.load(['block_structure'],'mod')[0]
assert SK.block_structure == pick1, 'loading SK block structure from file failed'
# check SumkDFT backward compatibility
sk_pick1 = BlockStructure(gf_struct_sumk = SK.gf_struct_sumk,
gf_struct_solver = SK.gf_struct_solver,
solver_to_sumk = SK.solver_to_sumk,
sumk_to_solver = SK.sumk_to_solver,
solver_to_sumk_block = SK.solver_to_sumk_block)
assert sk_pick1 == pick1, 'constructing block structure from SumkDFT properties failed'
# check pick_gf_struct_sumk
pick2 = original_bs.copy()
pick2.pick_gf_struct_sumk([{'up': [1, 2], 'down': [0,1]}])
# check map_gf_struct_solver
mapping = [{ ('down_0', 0):('down', 0),
('down_0', 1):('down', 2),
('down_1', 0):('down', 1),
('up_0', 0) :('down_1', 0),
('up_0', 1) :('up_0', 0) }]
map1 = original_bs.copy()
map1.map_gf_struct_solver(mapping)
# check create_gf
G1 = original_bs.create_gf(beta=40,n_points=3)
i = 1
for block,gf in G1:
gf << SemiCircular(i)
i+=1
# check approximate_as_diagonal
offd = original_bs.copy()
offd.approximate_as_diagonal()
# check map_gf_struct_solver
G2 = map1.convert_gf(G1,original_bs,beta=40,n_points=3,show_warnings=False)
# check full_structure
full = BlockStructure.full_structure([{'up_0': [0, 1], 'up_1': [0], 'down_1': [0], 'down_0': [0, 1]}],None)
# check __eq__
assert full==full, 'equality not correct (equal structures not equal)'
assert pick1==pick1, 'equality not correct (equal structures not equal)'
assert pick1!=pick2, 'equality not correct (different structures not different)'
assert original_bs!=offd, 'equality not correct (different structures not different)'
if mpi.is_master_node():
with HDFArchive('blockstructure.out.h5','w') as ar:
ar['original_bs'] = original_bs
ar['pick1'] = pick1
ar['pick2'] = pick2
ar['map1'] = map1
ar['offd'] = offd
ar['G1'] = G1
ar['G2'] = G2
ar['full'] = full
# cannot use h5diff because BlockStructure testing is not implemented
# there (and seems difficult to implement because it would mix triqs
# and dft_tools)
with HDFArchive('blockstructure.out.h5','r') as ar,\
HDFArchive('blockstructure.ref.h5','r') as ar2:
for k in ar2:
if isinstance(ar[k],BlockGf):
assert_block_gfs_are_close(ar[k],ar2[k],1.e-6)
else:
assert ar[k]==ar2[k], '{} not equal'.format(k)

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3
test/sigma_from_file.py
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@ -51,5 +51,4 @@ SK.set_Sigma([Sigma_txt])
SK.hdf_file = 'sigma_from_file.out.h5'
SK.save(['Sigma_imp_w'])
if ((Sigma_txt - Sigma_hdf).real < 1e-6) & ((Sigma_txt - Sigma_hdf).imag < 1e-6):
print 'Conversion: HDF -> TRIQS -> TXT -> TRIQS successful!'
assert_block_gfs_are_close(Sigma_txt, Sigma_hdf)