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minor doc fixes

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Alexander Hampel 2023-06-19 11:03:56 -04:00
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8
doc/guide/analysis.rst
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@ -83,7 +83,7 @@ For plotting the density of states, you type::
SK.density_of_states(mu, broadening, mesh, with_Sigma, with_dc, proj_type, dosocc, save_to_file)
where a brief description of all of the inputs are given in :meth:`density_of_states <dft.sumk_dft_tools.SumkDFTTools.density_of_states>`, which a more in depth discussion of using this routine is given here.
where a description of all of the inputs are given in :meth:`density_of_states <dft.sumk_dft_tools.SumkDFTTools.density_of_states>`:
.. automethod:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools.density_of_states
:noindex:
@ -92,7 +92,7 @@ where a brief description of all of the inputs are given in :meth:`density_of_st
:width: 600
:align: center
The figure above shows the DFT SrVO\ :sub:`3`\ density of states generated from 2925 k-points in the irreducible Brillouin zone with the V t\ :sub:`2g`\ Wanner projectors generated within a correlated energy window of [-13.6, 13.6] eV. The `broadening` input has been set to the temperature (i.e., 1/Beta). The total, V t\ :sub:`2g`\ Wannier and occupied total density of states generated from the SK.density_of_states() routine are shown. Note that the noise in the density of states comes from the number of k-points used. This can be removed upon by either using more k-points or using a larger `broadening` value.
The figure above shows the DFT SrVO\ :sub:`3`\ density of states generated from 2925 k-points in the irreducible Brillouin zone with the V t\ :sub:`2g`\ Wannier projectors generated within a correlated energy window of [-13.6, 13.6] eV. The `broadening` input has been set to the temperature (i.e., 1/Beta). The total, V t\ :sub:`2g`\ Wannier and occupied total density of states generated from the SK.density_of_states() routine are shown. Note that the noise in the density of states comes from the number of k-points used. This can be removed upon by either using more k-points or using a larger `broadening` value.
Band resolved density matrices
@ -123,7 +123,7 @@ This spectral function is calculated by typing::
:width: 1000
:align: center
The figure above shows the DFT SrVO\ :sub:`3`\ spaghetti plot (generated using V t\ :sub:`2g`\ Wanner projectors generated within a correlated energy window of [-13.6, 13.6] eV). As before, the broadening input has been set to the temperature (i.e., 1/Beta). The left panel shows the total A(k, :math:`\omega`) whereas the right gives the Wannier A(k, :math:`\omega`), both generated from this SK.spaghettis().
The figure above shows the DFT SrVO\ :sub:`3`\ spaghetti plot (generated using V t\ :sub:`2g`\ Wannier projectors generated within a correlated energy window of [-13.6, 13.6] eV). As before, the broadening input has been set to the temperature (i.e., 1/Beta). The left panel shows the total A(k, :math:`\omega`) whereas the right gives the Wannier A(k, :math:`\omega`), both generated from this SK.spaghettis().
Energy contours of the k-resolved Spectral function
@ -142,7 +142,7 @@ This routine calculates the k-resolved spectral function evaluated at the Fermi
:width: 1000
:align: center
The figure above shows the DFT SrVO\ :sub:`3`\ energy contour plots (again, generated using V t\ :sub:`2g`\ Wanner projectors generated within a correlated energy window of [-13.6, 13,6] eV and broadening of 1/Beta). Both panels have been generated on a k-mesh within the first Brilluoin zone on the k\ :sub:`z`\ = 0.0 plane centered at the :math:`\Gamma` point. Here, each panel generated using the outputs from this SK.spectral_contours_plot() routine shows the A(k, :math:`\omega`) evaluated at :math:`\omega` = -0.5 eV (left) and the Fermi level, :math:`\omega` = 0.0 eV, (right).
The figure above shows the DFT SrVO\ :sub:`3`\ energy contour plots (again, generated using V t\ :sub:`2g`\ Wannier projectors generated within a correlated energy window of [-13.6, 13,6] eV and broadening of 1/Beta). Both panels have been generated on a k-mesh within the first Brillouin zone on the k\ :sub:`z`\ = 0.0 plane centered at the :math:`\Gamma` point. Here, each panel generated using the outputs from this SK.spectral_contours_plot() routine shows the A(k, :math:`\omega`) evaluated at :math:`\omega` = -0.5 eV (left) and the Fermi level, :math:`\omega` = 0.0 eV, (right).
Partial charges

2
doc/guide/conv_elk.rst
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@ -152,7 +152,7 @@ These outputs are converted to the HDF5 file by::
The kgrid and ngrid are user-defined numpy array inputs containing the plot3d inputs described above.
These inputs are needed to generate the reciprocal lattice coordinates for the output files.
The default for both of these variables is None, which in this case the converter automatically generates the
full Brilluoin zone by applying all of the symmetry operators to the read IBZ coordinates. However,
full Brillouin zone by applying all of the symmetry operators to the read IBZ coordinates. However,
if the plot3d input is a k-mesh not centered around the origin and/or a k-mesh which only requires
a subset of the symmetry operators (say a 2D k-mesh) then the plot3d input needs to be an input to
the converter. Here, kgrid would be a double numpy array of size (4,3) specifying the k-mesh corner,

2
doc/guide/transport.rst
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@ -168,7 +168,7 @@ Example
-------
Here we present an example calculation of the DFT optical conductivity of SrVO3 comparing the results from the Elk and Wien2k inputs. The DFT codes used 4495 k-points in the
irreducible Brillouin zone with Wanner projectors generated within a correlated energy window of [-8, 7.5] eV. We assume that the required DFT files have been read and saved by the TRIQS
irreducible Brillouin zone with Wannier projectors generated within a correlated energy window of [-8, 7.5] eV. We assume that the required DFT files have been read and saved by the TRIQS
interface routines as discussed previously. Below is an example script to generate the conductivities::
from sumk_dft_tools import *

127
python/triqs_dft_tools/sumk_dft_tools.py
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@ -55,16 +55,24 @@ class SumkDFTTools(SumkDFT):
def density_of_states(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, proj_type=None, dosocc=False, save_to_file=True):
"""
Calculates the density of states and the projected density of states.
Calculates the density of states and the projected density of states.
The basis of the projected density of states is specified by proj_type.
The output files (if `save_to_file = True`) have two (three in the orbital-resolved case) columns representing the frequency and real part of the DOS (and imaginary part of the DOS) in that order.
The output files are as follows:
- DOS_(spn).dat, the total DOS.
- DOS_(proj_type)_(spn)_proj(i).dat, the DOS projected to an orbital with index i which refers to the index given in SK.shells (or SK.corr_shells for proj_type = "wann").
- DOS_(proj_type)_(sp)_proj(i)_(m)_(n).dat, As above, but printed as orbitally-resolved matrix in indices "m" and "n". For example, for "d" orbitals, it gives the DOS separately for each orbital (e.g., `d_(xy)`, `d_(x^2-y^2)`, and so on).
Parameters
----------
mu : double, optional
Chemical potential, overrides the one stored in the hdf5 archive.
By default, this is automatically set to the chemical potential within the SK object.
broadening : double, optional
Lorentzian broadening of the spectra to avoid any numerical artifacts.
Lorentzian broadening of the spectra to avoid any numerical artifacts.
If not given, standard value of lattice_gf (0.001 eV) is used.
mesh : real frequency MeshType, optional
Omega mesh for the real-frequency Green's function.
@ -77,10 +85,11 @@ class SumkDFTTools(SumkDFT):
with_dc : boolean, optional
If True the double counting correction is used.
proj_type : string, optional
The type of projection used for the orbital-projected DOS.
These projected spectral functions will be determined alongside the total spectral function.
By default, no projected DOS type will be calculated (the corresponding projected arrays will be empty).
The type of projection used for the orbital-projected DOS.
These projected spectral functions will be determined alongside the total spectral function.
By default, no projected DOS type will be calculated (the corresponding projected arrays will be empty).
The following options are:
'None' - Only total DOS calculated
'wann' - Wannier DOS calculated from the Wannier projectors
'vasp' - Vasp orbital-projected DOS only from Vasp inputs
@ -98,18 +107,11 @@ class SumkDFTTools(SumkDFT):
Contains the full density of states with the form of DOS[spn][n_om] where "spn" speficies the spin type of the calculation ("up", "down", or combined "ud" which relates to calculations with spin-orbit coupling) and "n_om" is the number of real frequencies as specified by the real frequency MeshType used in the calculation. This array gives the total density of states.
DOSproj : Dict of numpy arrays
DOS projected to atom (shell) with the form of DOSproj[n_shells][spn][n_om] where "n_shells" is the total number of correlated or uncorrelated shells (depending on the input "proj_type"). This array gives the trace of the orbital-projected density of states. Empty if proj_type = None
DOSproj_orb : Dict of numpy arrays
DOSproj_orb : Dict of numpy arrays
Orbital-projected DOS projected to atom (shell) and resolved into orbital contributions with the form of DOSproj_orb[n_shells][spn][n_om,dim,dim] where "dim" specifies the orbital dimension of the correlated/uncorrelated shell (depending on the input "proj_type").
Empty if proj_type = None
The output files (if `save_to_file = True`) have two (three in the orbital-resolved case) columns representing the frequency and real part of the DOS (and imaginary part of the DOS) in that order.
The output files are as follows:
DOS_(spn).dat : The total DOS.
DOS_(proj_type)_(spn)_proj(i).dat : The DOS projected to an orbital with index i which refers to the index given in SK.shells (or SK.corr_shells for proj_type = "wann").
DOS_(proj_type)_(sp)_proj(i)_(m)_(n).dat: As above, but printed as orbitally-resolved matrix in indices "m" and "n". For example, for "d" orbitals, it gives the DOS separately for each orbital (e.g., "d_(xy)", "d_(x^2-y^2), and so on).
"""
# Note the proj_type = 'elk' (- Elk orbital-projected DOS only from Elk inputs) is not included for now.
# Brief description to why can be found in the comment above the currently commented out dft_band_characters() routine
# in converters/elk.py.
@ -181,7 +183,7 @@ class SumkDFTTools(SumkDFT):
# subgroup_present, values_not_read = self.read_input_from_hdf(
# subgrp=self.bc_data, things_to_read=things_to_read)
# if len(values_not_read) > 0 and mpi.is_master_node:
# raise ValueError(
# raise ValueError(
# 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read)
# set-up output arrays
@ -284,6 +286,7 @@ class SumkDFTTools(SumkDFT):
"""
Internal routine which calculates the project Green's function subject to the
proj_type input.
Parameters
----------
G_latt : Gf
@ -306,6 +309,7 @@ class SumkDFTTools(SumkDFT):
projected/downfolded lattice Green's function
Contains the band-resolved density matrices per k-point.
"""
# Note the proj_type = 'elk' (- Elk orbital-projected DOS only from Elk inputs) is not included for now.
# Brief description to why can be found in the comment above the currently commented out dft_band_characters() routine
# in converters/elk.py.
@ -354,6 +358,7 @@ class SumkDFTTools(SumkDFT):
"""
Internal routine which loads the n_parproj, proj_mat_all, rot_mat_all and
rot_mat_all_time_inv from parproj data from .h5 file.
Parameters
----------
data_type : string, optional
@ -361,6 +366,7 @@ class SumkDFTTools(SumkDFT):
'band' - reads data converted by bands_convert()
None - reads data converted by parproj_convert()
"""
# read in the projectors
things_to_read = ['n_parproj', 'proj_mat_all']
if data_type == 'band':
@ -399,7 +405,7 @@ class SumkDFTTools(SumkDFT):
save_occ : boolean, optional
If True, saves the band resolved density matrix in misc_data.
save_to_file : boolean, optional
If True, text files with the calculated data will be created.\
If True, text files with the calculated data will be created.
Returns
-------
@ -451,13 +457,23 @@ class SumkDFTTools(SumkDFT):
Calculates the correlated spectral function at the Fermi level (relating to the Fermi
surface) or at specific frequencies.
The output files have three columns representing the k-point index, frequency and A(k,w) in that order. The output files are as follows:
* `Akw_(sp).dat`, the total A(k,w)
* `Akw_(proj_type)_(spn)_proj(i).dat`, the A(k,w) projected to shell with index (i).
* `Akw_(proj_type)_(spn)_proj(i)_(m)_(n).dat`, as above, but for each (m) and (n) orbital contribution.
The files are prepended with either of the following:
For `FS` set to True the output files name include _FS_ and these files contain four columns which are the cartesian reciprocal coordinates (kx, ky, kz) and Akw.
For `FS` set to False the output files name include _omega_(iom) (with `iom` being the frequency mesh index). These files also contain four columns as described above along with a comment at the top of the file which gives the frequency value at which the spectral function was evaluated.
Parameters
----------
mu : double, optional
Chemical potential, overrides the one stored in the hdf5 archive.
By default, this is automatically set to the chemical potential within the SK object.
broadening : double, optional
Lorentzian broadening of the spectra to avoid any numerical artifacts.
Lorentzian broadening of the spectra to avoid any numerical artifacts.
If not given, standard value of lattice_gf (0.001 eV) is used.
mesh : real frequency MeshType, optional
Omega mesh for the real-frequency Green's function.
@ -479,39 +495,30 @@ class SumkDFTTools(SumkDFT):
with_dc : boolean, optional
If True the double counting correction is used.
proj_type : string, optional
The type of projection used for the orbital-projected DOS.
These projected spectral functions will be determined alongside the total spectral function.
By default, no projected DOS type will be calculated (the corresponding projected arrays will be empty).
The following options are:
'None' - Only total DOS calculated
'wann' - Wannier DOS calculated from the Wannier projectors
The type of projection used for the orbital-projected DOS.
These projected spectral functions will be determined alongside the total spectral function.
By default, no projected DOS type will be calculated (the corresponding projected arrays will be empty).
The following options are:
* `None` Only total DOS calculated
* `wann` Wannier DOS calculated from the Wannier projectors
save_to_file : boolean, optional
If True, text files with the calculated data will be created.
Returns
-------
Akw : Dict of numpy arrays
(Correlated) k-resolved spectral function.
This dictionary has the form of `Akw[spn][n_k, n_om]` where spn, n_k and n_om are the spin, number of k-points, and number of frequencies used in the calculation.
pAkw : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms (i.e., the Trace of the orbital-projected A(k,w)).
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om] where n_shells is the total number of correlated or uncorrelated shells.
Empty if proj_type = None
pAkw_orb : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions.
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om,dim,dim] where dim specifies the orbital dimension of the correlated/uncorrelated shell.
Empty if proj_type = None
The output files have three columns representing the k-point index, frequency and A(k,w) in that order. The output files are as follows:
Akw_(sp).dat : The total A(k,w).
Akw_(proj_type)_(spn)_proj(i).dat: The A(k,w) projected to shell with index (i).
Akw_(proj_type)_(spn)_proj(i)_(m)_(n).dat`: As above, but for each (m) and (n) orbital contribution.
The files are prepended with either of the following:
For `FS` set to True : The output files' name include _FS_ and these files contain four columns which are the cartesian reciprocal coordinates (kx, ky, kz) and Akw.
For `FS` set to False : The output files' name include _omega_(iom) (with `iom` being the frequency mesh index). These files also contain four columns as described above along with a comment at the top of the file which gives the frequency value at which the spectral function was evaluated.
Akw : Dict of numpy arrays
(Correlated) k-resolved spectral function.
This dictionary has the form of `Akw[spn][n_k, n_om]` where spn, n_k and n_om are the spin, number of k-points, and number of frequencies used in the calculation.
pAkw : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms (i.e., the Trace of the orbital-projected A(k,w)).
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om] where n_shells is the total number of correlated or uncorrelated shells. Empty if `proj_type = None`
pAkw_orb : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions.
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om,dim,dim] where dim specifies the orbital dimension of the correlated/uncorrelated shell. Empty if `proj_type = None`
"""
if (proj_type != None):
assert proj_type in ('wann'), "'proj_type' must be 'wann' if not None"
# read in the energy contour energies and projectors
@ -631,6 +638,14 @@ class SumkDFTTools(SumkDFT):
"""
Calculates the k-resolved spectral function A(k,w) (band structure)
The output files have three columns representing the k-point index, frequency and A(k,w) (in this order).
The output files are as follows:
- Akw_(sp).dat, the total A(k,w).
- Akw_(proj_type)_(spn)_proj(i).dat, the A(k,w) projected to shell with index (i).
- Akw_(proj_type)_(spn)_proj(i)_(m)_(n).dat, as above, but for each (m) and (n) orbital contribution.
Parameters
----------
mu : double, optional
@ -640,7 +655,7 @@ class SumkDFTTools(SumkDFT):
Lorentzian broadening of the spectra to avoid any numerical artifacts.
If not given, standard value of lattice_gf (0.001 eV) is used.
mesh : real frequency MeshType, optional
Omega mesh for the real-frequency Green's function.
Omega mesh for the real-frequency Green's function.
Given as parameter to lattice_gf.
plot_shift : double, optional
Offset [=(ik-1)*plot_shift, where ik is the index of the k-point] for each A(k,w) for stacked plotting of spectra.
@ -652,7 +667,7 @@ class SumkDFTTools(SumkDFT):
is calculated for.
If shell_list = None and proj_type is not None, then the projected spectral
function is calculated for all shells.
Note for experts: The spectra from Wien2k inputs are not rotated to the local coordinate system used in Wien2k.
Note for experts: The spectra from Wien2k inputs are not rotated to the local coordinate system used in Wien2k.
with_Sigma : boolean, optional
If True, the self energy is used for the calculation.
If false, the DOS is calculated without self energy.
@ -661,10 +676,11 @@ class SumkDFTTools(SumkDFT):
with_dc : boolean, optional
If True the double counting correction is used.
proj_type : string, optional
The type of projection used for the orbital-projected DOS.
These projected spectral functions will be determined alongside the total spectral function.
By default, no projected DOS type will be calculated (the corresponding projected arrays will be empty).
The type of projection used for the orbital-projected DOS.
These projected spectral functions will be determined alongside the total spectral function.
By default, no projected DOS type will be calculated (the corresponding projected arrays will be empty).
The following options are:
'None' - Only total DOS calculated
'wann' - Wannier DOS calculated from the Wannier projectors
'wien2k' - Wien2k orbital-projected DOS from the wien2k theta projectors
@ -675,21 +691,16 @@ class SumkDFTTools(SumkDFT):
-------
Akw : Dict of numpy arrays
(Correlated) k-resolved spectral function.
This dictionary has the form of `Akw[spn][n_k, n_om]` where spn, n_k and n_om are the spin, number of k-points, and number of frequencies used in the calculation.
This dictionary has the form of `Akw[spn][n_k, n_om]` where spn, n_k and n_om are the spin, number of k-points, and number of frequencies used in the calculation.
pAkw : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms (i.e., the Trace of the orbital-projected A(k,w)).
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om] where n_shells is the total number of correlated or uncorrelated shells.
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om] where n_shells is the total number of correlated or uncorrelated shells.
Empty if proj_type = None
pAkw_orb : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions.
This dictionary has the form of pAkw[n_shells][spn][n_k, n_om,dim,dim] where dim specifies the orbital dimension of the correlated/uncorrelated shell.
Empty if proj_type = None
The output files have three columns representing the k-point index, frequency and A(k,w) in that order. The output files are as follows:
Akw_(sp).dat : The total A(k,w).
Akw_(proj_type)_(spn)_proj(i).dat: The A(k,w) projected to shell with index (i).
Akw_(proj_type)_(spn)_proj(i)_(m)_(n).dat`: As above, but for each (m) and (n) orbital contribution.
"""
# initialisation
@ -785,7 +796,7 @@ class SumkDFTTools(SumkDFT):
def gen_Akw(self, mu, broadening, mesh, plot_shift, plot_range, shell_list, with_Sigma, with_dc, proj_type):
"""
Internal routine used by spaghettis and spectral_contours to Calculate the k-resolved spectral
Internal routine used by spaghettis and spectral_contours to Calculate the k-resolved spectral
function A(k,w). For advanced users only.
Parameters