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doc, log and minor updates

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Alyn James 2023-06-19 14:34:47 +01:00
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6
doc/ChangeLog.md
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@ -4,6 +4,12 @@
## unstable ## unstable
* updated github work flow to match triqs unstable requisites
* sumk_dft_tools.py rewritten to have single routines to calculate DOS, spaghettis and (Elk specific for now) spectral contours
* occupied DOS can be calculated (sumk_dft_tools.occupations() is needed to be calculated first)
* analysis.rst and conv_elk.rst updated to improve routine descriptions and includes example figures
* updated Elk tests and rewritten test scripts (.h5 files remain unchanged)
* New converter routines to read in Elk data for sumk_dft_tools.spectral_contours() (Elk k-mesh generator and checker needs to be optimized as it's currently slow). commented out Elk "bandcharacter" conversion from Elk converter and Elk DFT+DMFT PDOS code which used it (this method needs to be checked)
* SumK requires now to pass a mesh on init to clarify the mesh on which it operates * SumK requires now to pass a mesh on init to clarify the mesh on which it operates
* rename / unify name of `sumk.Sigma_imp_iw` and `sumk.Sigma_imp_w` -> `sumk.Sigma_imp` * rename / unify name of `sumk.Sigma_imp_iw` and `sumk.Sigma_imp_w` -> `sumk.Sigma_imp`
* remove `iw_or_w` arguments * remove `iw_or_w` arguments

73
doc/guide/analysis.rst
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@ -88,40 +88,13 @@ where a brief description of all of the inputs are given in :meth:`density_of_st
.. automethod:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools.density_of_states .. automethod:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools.density_of_states
:noindex: :noindex:
Input parameter breakdown:
* `mu` (Optional, default is None): The `mu` input specifies the chemical potential to be used in the calculation. By default, this is automatically set to the chemical potential within the SK object.
* `broadening` (Optional, default 0.01 eV). Traditionally, a small imaginary part is included for a non-interacting spectral function to avoid any numerical artifacts. The user can specify this imaginary part with the `broadening` input. The default value of `0.01 eV` if there is no `broadening` or `mesh` input.
* `mesh` (Optional, default is None): The `mesh` input requires a real frequency MeshType variable to specificy the frequency on which the spectral function is evaluated on. If the real frequency self-energy is used, then the associated mesh of the self-energy will be used instead. However, this `mesh` input will superseed the SK.mesh real frequency MeshType if it exists.
* `with_Sigma` and `with_dc` (Optional, both set to True by default): These Boolean options determine whether to include the real frequency self-energy (`with_Sigma`) and double counting term (`with_dc`) from the DMFT calculation. To calculate the DFT+DMFT DOS, both options need to be set to True. If both are set to false, then the DFT DOS will be calculated instead.
* `proj_type` (Optional, default is None): The type of projection used for the orbital-projected DOS is specified by the optional `proj_type`. 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). A full description of the DFT-code dependent options is given below.
* `dosocc` (Optional, default is False): The occupied part of the spectral function can be generated by setting `dosocc` to True. As a prerequisite to using this option, the user must first calculate the band-resolved density matrix (or occupations) by calling :meth:`occupations <dft.sumk_dft_tools.SumkDFTTools.occupations>` with the Matsubara self-energy.
* `save_to_file` (Optional, default is True): To save the generated DOS from this routine, then the optional `save_to_file` must be set to True.
Variables returned from this function:
* DOS - this is a dictionary of numpy arrays 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 - A dictionary of numpy arrays with the form of `DOSproj[n_shells][spn][n_om]` where `spn` and `n_om` are given above and `n_shells` are the total number of correlated or uncorrelated shells (depending on the input `dos_type`). This array gives the trace of the orbital-projected density of states.
* DOSproj_orb - A dictionary of numpy arrays with the form of `DOSproj_orb[n_shells][spn][n_om,dim,dim]` where the variables are defined as given previously with `dim` specifying the orbital dimension of the correlated/uncorrelated shell (depending on the input `dos_type`). This array gives the orbital-projected density of states.
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_(sp).dat`: The total DOS, where `(dos_type)` and `(sp)` have been defined previously.
* `DOS_(proj_type)_(sp)_proj(i).dat`: The DOS projected to an orbital with index `(i)`. The index `(i)` refers to tprojindices 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 `d` orbitals, it gives the DOS separately for, e.g., :math:`d_{xy}`, :math:`d_{x^2-y^2}`, and so on.
The different DFT code interfaces read in different variables needed to generate other options for the string type `proj_type` are as follows:
* "wann" - calculates the Wannier projected DOS.
* "vasp" - calculates the projected DOS from the projectors generated within Vasp.
* "wien2k" - calculates the projected DOS from the theta projectors generated from dmftproj used to interface Wien2k with TRIQS.
.. image:: images_scripts/DFT_Tools_SVO_DFT_DOS.png .. image:: images_scripts/DFT_Tools_SVO_DFT_DOS.png
:width: 600 :width: 600
:align: center :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`\ 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.
Band resolved density matrices Band resolved density matrices
------------------------------ ------------------------------
@ -133,8 +106,6 @@ This is done by calling the following::
This is required to generate the occupied DOS in SK.density_of_states() when dosocc is set to True. The `save_occ` optional input (True by default) saves these density matrices to the HDF5 file within the misc_data subgroup. The other variables are the same as defined above. See :meth:`occupations <dft.sumk_dft_tools.SumkDFTTools.occupations>` This is required to generate the occupied DOS in SK.density_of_states() when dosocc is set to True. The `save_occ` optional input (True by default) saves these density matrices to the HDF5 file within the misc_data subgroup. The other variables are the same as defined above. See :meth:`occupations <dft.sumk_dft_tools.SumkDFTTools.occupations>`
Momentum resolved spectral function (with real-frequency self energy) Momentum resolved spectral function (with real-frequency self energy)
--------------------------------------------------------------------- ---------------------------------------------------------------------
@ -145,26 +116,8 @@ This spectral function is calculated by typing::
SK.spaghettis(mu, broadening, mesh, plot_shift, plot_range, shell_list, with_Sigma, with_dc, proj_type, save_to_file) SK.spaghettis(mu, broadening, mesh, plot_shift, plot_range, shell_list, with_Sigma, with_dc, proj_type, save_to_file)
Input variables such as `mu`, `broadening` and so on have the same definition as given previously. .. automethod:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools.spaghettis
:noindex:
The additional parameters are defined as follows:
* `plot_shift` (Optional, default is 0.0): An additional shift added as `(ik-1)*plot_shift`, where `ik` is the index of the `k` point. This is useful for plotting purposes.
* `plot_range` (Optional, default is None): A list with two entries, :math:`\omega_{min}` and :math:`\omega_{max}`, which set the plot range for the output. By default, the full momentum range as given in the self_energy.mesh, input mesh, or SK.mesh is used.
* `shell_list` (Optional, default is None): A list of integers denoting the shell indices onto which the spectral function is projected if `proj_type` is not None. The resulting function is saved in the files. By default, the projected spectral function is generated for all shells if `proj_type` is not None. Note for experts: The spectra are not rotated to the local coordinate system used in Wien2k.
* `proj_type` : This has the same definition as above but with only the "wann" and "wien2k" options implemented.
Variables returned from this function:
* `Akw` - this is a dictionary of numpy arrays with the form of `Akw[spn][n_ik, n_om]` where `n_k` is the number of k-points used in the calculation. This array gives the total A(k, :math:`\omega`).
* `pAkw` - A dictionary of numpy arrays with the form of `pAkw[n_shells][spn][n_k, n_om]` where `spn`, `n_om` and `n_shells` have been defined previously. This array gives the trace of the orbital-projected A(k, :math:`\omega`).
* `pAkw_orb` - A dictionary of numpy arrays with the form of `pAkw_orb[n_shells][spn][n_om,dim,dim]` where the variables have been previously defined. This array gives the orbital-projected A(k, :math:`\omega`).
The output files (if `save_to_file = True`) have three columns representing the k-point index, frequency and A(k, :math:`\omega`) in that order. The output files are as follows:
* `Akw_(sp).dat`: The total A(k, :math:`\omega`).
* `Akw_(dos_type)_(sp)_proj(i).dat`: The A(k, :math:`\omega`) projected to shell with index `(i)` (same as defined in the DOS output files).
* `Akw_(dos_type)_(sp)_proj(i)_(m)_(n).dat`: As above, but printed as orbitally-resolved matrix in indices `(m)` and `(n)`.
Also see :meth:`spaghettis <dft.sumk_dft_tools.SumkDFTTools.spaghettis>`.
.. image:: images_scripts/DFT_Tools_SVO_DFT_spaghettis.png .. image:: images_scripts/DFT_Tools_SVO_DFT_spaghettis.png
:width: 1000 :width: 1000
@ -182,24 +135,8 @@ This routine calculates the k-resolved spectral function evaluated at the Fermi
SK.spectral_contours(mu, broadening, mesh, plot_range, FS, with_Sigma, with_dc, proj_type, save_to_file) SK.spectral_contours(mu, broadening, mesh, plot_range, FS, with_Sigma, with_dc, proj_type, save_to_file)
Again, certain inputs in this routine have already been defined. Note that only proj_type="wann" has been implemented for this routine. .. automethod:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools.spectral_contours
:noindex:
Below gives a description of the other inputs used here:
* `FS` (Optional, default is True): If True, this outputs the spectral function evaluated at the Fermi level (or the frequency value closest to 0.0 eV in the given mesh). If false, then the spectral function is evaluated at the frequency values within the frequency mesh used (or within `plot_range` if specified).
This routine returns the following:
* `Akw` - A dictionary of numpy arrays with the form of `Akw[spn][n_ik, n_om]` where `spn`, `n_k` and `n_om` being defined as given above. This array gives the total A(k, :math:`\omega`).
* `pAkw` - A dictionary of numpy arrays with the form of `pAkw[n_shells][spn][n_k, n_om]` (`n_shells` defined above). This array gives the trace of the orbital-projected A(k, :math:`\omega`).
* `pAkw_orb` - A dictionary of numpy arrays with the form of `pAkw_orb[n_shells][spn][n_om,dim,dim]` (`dim` defined above). This array gives the orbital-projected A(k, :math:`\omega`).
The output files will have the same extensions of `_(sp)_proj(i)_(m)_(n).dat`, `_(sp)_proj(i)_(m)_(n).dat` and `_(sp)_proj(i)_(m)_(n).dat` as described in the Spaghettis routine.
The files are prepended with either of the following:
* For `FS` set to True : The output files' name are prepended with `Akw_FS` and these files contain four columns which are the `k`\ :sub:`x`\, `k`\ :sub:`y`\, `k`\ :sub:`z`\, and `Akw`. Here (`k`\ :sub:`x`\, `k`\ :sub:`y`\, `k`\ :sub:`z`\) are the cartesian reciprocal coordinates,
* For `FS` set to False : The output files' name are prepended with `Akw_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 :math:`\omega` frequency value at which the spectral function was evaluated.
Also see :meth:`spectral_contours <dft.sumk_dft_tools.SumkDFTTools.spectral_contours>`
.. image:: images_scripts/DFT_Tools_SVO_DFT_energy_contours.png .. image:: images_scripts/DFT_Tools_SVO_DFT_energy_contours.png
:width: 1000 :width: 1000

7
python/triqs_dft_tools/converters/elk.py
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@ -626,7 +626,12 @@ class ElkConverter(ConverterTools,Elk_tools,read_Elk):
del ar del ar
mpi.report('Converted the Contours data') mpi.report('Converted the Contours data')
#commented out for now - unsure using this produces DFT+DMFT PDOS. # commented out for now - unsure using this produces DFT+DMFT PDOS.
# The data from BC.OUT are the band-resolved diagonal muffin-tin DFT density matrix elements used in Elk to calculate PDOS
# (the PDOS is calculated from the Trace over the bands indices). Although this is equivalent to using using projectors in DFT and is likely valid for DFT+DMFT,
# the equivalence needs to be thoroughly checked for DFT+DMFT, but would require theta (or similar) projectors from Elk to do so.
# code left here just in case.
# def dft_band_characters(self): # def dft_band_characters(self):
# """ # """
# Reads in the band-resolved muffin-tin density matrix (band characters) generated in Elk # Reads in the band-resolved muffin-tin density matrix (band characters) generated in Elk

145
python/triqs_dft_tools/sumk_dft_tools.py
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@ -62,40 +62,58 @@ class SumkDFTTools(SumkDFT):
---------- ----------
mu : double, optional mu : double, optional
Chemical potential, overrides the one stored in the hdf5 archive. 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 broadening : double, optional
Lorentzian broadening of the spectra. Lorentzian broadening of the spectra to avoid any numerical artifacts.
If not given, standard value of lattice_gf is used. If not given, standard value of lattice_gf (0.001 eV) is used.
mesh : real frequency MeshType, optional 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. Given as parameter to lattice_gf.
with_Sigma : boolean, optional with_Sigma : boolean, optional
If True, the self energy is used for the calculation. If True, the self energy is used for the calculation.
If false, the DOS is calculated without self energy. If false, the DOS is calculated without self energy.
Both with_Sigma and with_dc equal to True is needed for DFT+DMFT A(w) calculated.
Both with_Sigma and with_dc equal to false is needed for DFT A(w) calculated.
with_dc : boolean, optional with_dc : boolean, optional
If True the double counting correction is used. If True the double counting correction is used.
proj_type : string, optional proj_type : string, optional
Output the orbital-projected DOS type from the following options: 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 'wann' - Wannier DOS calculated from the Wannier projectors
'vasp' - Vasp orbital-projected DOS only from Vasp inputs 'vasp' - Vasp orbital-projected DOS only from Vasp inputs
'wien2k' - Wien2k orbital-projected DOS from the wien2k theta projectors 'wien2k' - Wien2k orbital-projected DOS from the wien2k theta projectors
'elk' - Elk orbital-projected DOS only from Elk inputs
dosocc : boolean, optional dosocc : boolean, optional
If True, the occupied DOS, DOSproj and DOSproj_orb will be returned. If True, the occupied DOS, DOSproj and DOSproj_orb will be returned.
The prerequisite of this option is to have calculated the band-resolved The prerequisite of this option is to have calculated the band-resolved
density matrices generated by occupations(). density matrices generated by the occupations() routine.
save_to_file : boolean, optional 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 Returns
------- -------
DOS : Dict of numpy arrays DOS : Dict of numpy arrays
Contains the full density of states. 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 DOSproj : Dict of numpy arrays
DOS projected to atoms. Empty if proj_type = None 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
DOS projected to atoms and resolved into orbital contributions. 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 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.
# code left here just in case it will be reused.
if (proj_type != None): if (proj_type != None):
# assert proj_type in ('wann', 'vasp','wien2k','elk'), "'proj_type' must be either 'wann', 'vasp', 'wien2k', or 'elk'" # assert proj_type in ('wann', 'vasp','wien2k','elk'), "'proj_type' must be either 'wann', 'vasp', 'wien2k', or 'elk'"
assert proj_type in ('wann', 'vasp', 'wien2k', assert proj_type in ('wann', 'vasp', 'wien2k',
@ -281,15 +299,17 @@ class SumkDFTTools(SumkDFT):
'wann' - Wannier DOS calculated from the Wannier projectors 'wann' - Wannier DOS calculated from the Wannier projectors
'vasp' - Vasp orbital-projected DOS only from Vasp inputs 'vasp' - Vasp orbital-projected DOS only from Vasp inputs
'wien2k' - Wien2k orbital-projected DOS from the wien2k theta projectors 'wien2k' - Wien2k orbital-projected DOS from the wien2k theta projectors
'elk' - Elk orbital-projected DOS only from Elk inputs
Returns Returns
------- -------
G_proj : Gf G_proj : Gf
projected/downfolded lattice Green's function projected/downfolded lattice Green's function
Contains the band-resolved density matrices per k-point. 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.
# code left here just in case it will be reused.
G_proj = G_inp.copy() G_proj = G_inp.copy()
if (proj_type == 'wann'): if (proj_type == 'wann'):
for bname, gf in G_proj: for bname, gf in G_proj:
@ -435,40 +455,62 @@ class SumkDFTTools(SumkDFT):
---------- ----------
mu : double, optional mu : double, optional
Chemical potential, overrides the one stored in the hdf5 archive. 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 broadening : double, optional
Lorentzian broadening of the spectra. Lorentzian broadening of the spectra to avoid any numerical artifacts.
If not given, standard value of lattice_gf is used. If not given, standard value of lattice_gf (0.001 eV) is used.
mesh : real frequency MeshType, optional 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. 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.
plot_range : list of double, optional plot_range : list of double, optional
Sets the energy window for plotting to (plot_range[0],plot_range[1]). Sets the energy window for plotting to (plot_range[0],plot_range[1]).
If not provided, the min and max values of the energy mesh is used. If not provided, the min and max values of the energy mesh is used.
FS : boolean FS : boolean
Flag for calculating the spectral function at the Fermi level (omega ~ 0) Flag for calculating the spectral function at the Fermi level (omega ~ 0)
If False, the spectral function will be generated for each frequency within If False, the spectral function will be generated for each frequency within
plot_range. plot_range.
with_Sigma : boolean, optional with_Sigma : boolean, optional
If True, the self energy is used for the calculation. If True, the self energy is used for the calculation.
If false, the DOS is calculated without self energy. If false, the DOS is calculated without self energy.
Both with_Sigma and with_dc equal to True is needed for DFT+DMFT A(k,w) calculated.
Both with_Sigma and with_dc equal to false is needed for DFT A(k,w) calculated.
with_dc : boolean, optional with_dc : boolean, optional
If True the double counting correction is used. If True the double counting correction is used.
proj_type : string, optional proj_type : string, optional
Output the orbital-projected A(k,w) type from the following: The type of projection used for the orbital-projected DOS.
'wann' - Wannier A(k,w) calculated from the Wannier projectors 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 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 Returns
------- -------
Akw : Dict of numpy arrays Akw : Dict of numpy arrays
(Correlated) k-resolved spectral function (Correlated) k-resolved spectral function.
pAkw : Dict of numpy arrays 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.
(Correlated) k-resolved spectral function projected to atoms. 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 Empty if proj_type = None
pAkw_orb : Dict of numpy arrays pAkw_orb : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms and (Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions. Empty if proj_type = None 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.
""" """
if (proj_type != None): if (proj_type != None):
assert proj_type in ('wann'), "'proj_type' must be 'wann' if not None" assert proj_type in ('wann'), "'proj_type' must be 'wann' if not None"
@ -573,9 +615,6 @@ class SumkDFTTools(SumkDFT):
dim = len(pAkw_orb[ish][sp][0, 0, 0, :]) dim = len(pAkw_orb[ish][sp][0, 0, 0, :])
for i in range(dim): for i in range(dim):
for j in range(dim): for j in range(dim):
# For Elk with parproj - skip off-diagonal elements
if (proj_type == 'elk') and (i != j):
continue
strng2 = strng + '_' + str(i) + '_' + str(j) strng2 = strng + '_' + str(i) + '_' + str(j)
# Open file for storage: # Open file for storage:
f = open(strng2 + '.dat', 'w') f = open(strng2 + '.dat', 'w')
@ -596,14 +635,15 @@ class SumkDFTTools(SumkDFT):
---------- ----------
mu : double, optional mu : double, optional
Chemical potential, overrides the one stored in the hdf5 archive. 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 broadening : double, optional
Lorentzian broadening of the spectra. Lorentzian broadening of the spectra to avoid any numerical artifacts.
If not given, standard value of lattice_gf is used. If not given, standard value of lattice_gf (0.001 eV) is used.
mesh : real frequency MeshType, optional 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. Given as parameter to lattice_gf.
plot_shift : double, optional plot_shift : double, optional
Offset for each A(k,w) for stacked plotting of spectra. Offset [=(ik-1)*plot_shift, where ik is the index of the k-point] for each A(k,w) for stacked plotting of spectra.
plot_range : list of double, optional plot_range : list of double, optional
Sets the energy window for plotting to (plot_range[0],plot_range[1]). Sets the energy window for plotting to (plot_range[0],plot_range[1]).
If not provided, the min and max values of the energy mesh is used. If not provided, the min and max values of the energy mesh is used.
@ -612,28 +652,44 @@ class SumkDFTTools(SumkDFT):
is calculated for. is calculated for.
If shell_list = None and proj_type is not None, then the projected spectral If shell_list = None and proj_type is not None, then the projected spectral
function is calculated for all shells. 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.
with_Sigma : boolean, optional with_Sigma : boolean, optional
If True, the self energy is used for the calculation. If True, the self energy is used for the calculation.
If false, the DOS is calculated without self energy. If false, the DOS is calculated without self energy.
Both with_Sigma and with_dc equal to True is needed for DFT+DMFT A(k,w) calculated.
Both with_Sigma and with_dc equal to false is needed for DFT A(k,w) calculated.
with_dc : boolean, optional with_dc : boolean, optional
If True the double counting correction is used. If True the double counting correction is used.
proj_type : string, optional proj_type : string, optional
Output the orbital-projected A(k,w) type from the following: The type of projection used for the orbital-projected DOS.
'wann' - Wannier A(k,w) calculated from the Wannier projectors These projected spectral functions will be determined alongside the total spectral function.
'wien2k' - Wien2k orbital-projected A(k,w) from the wien2k theta projectors 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
save_to_file : boolean, optional 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 Returns
------- -------
Akw : Dict of numpy arrays Akw : Dict of numpy arrays
(Correlated) k-resolved spectral function (Correlated) k-resolved spectral function.
pAkw : Dict of numpy arrays 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.
(Correlated) k-resolved spectral function projected to atoms. 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 Empty if proj_type = None
pAkw_orb : Dict of numpy arrays pAkw_orb : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms and (Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions. Empty if proj_type = None 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 # initialisation
@ -714,9 +770,6 @@ class SumkDFTTools(SumkDFT):
dim = len(pAkw_orb[ish][sp][0, 0, 0, :]) dim = len(pAkw_orb[ish][sp][0, 0, 0, :])
for i in range(dim): for i in range(dim):
for j in range(dim): for j in range(dim):
# For Elk with parproj - skip off-diagonal elements
if(proj_type =='elk') and (i!=j):
continue
# Open file for storage: # Open file for storage:
f = open('Akw_' + proj_type + '_' + sp + '_proj' + str(jsh) f = open('Akw_' + proj_type + '_' + sp + '_proj' + str(jsh)
+ '_' + str(i) + '_' + str(j) + '.dat', 'w') + '_' + str(i) + '_' + str(j) + '.dat', 'w')

3
test/python/srvo3_spectral.py
View File

@ -13,11 +13,8 @@ SK.chemical_potential = chemical_potential
SK.dc_imp = dc_imp SK.dc_imp = dc_imp
SK.set_Sigma([Sigma]) SK.set_Sigma([Sigma])
#dos_wannier = SK.dos_wannier_basis(broadening=0.01, with_Sigma=True, with_dc=True, save_to_file=False)
#dos_parproj = SK.dos_parproj_basis(broadening=0.01, with_Sigma=True, with_dc=True, save_to_file=False)
dos_wannier = SK.density_of_states(broadening=0.01, with_Sigma=True, with_dc=True, proj_type='wann', save_to_file=False) dos_wannier = SK.density_of_states(broadening=0.01, with_Sigma=True, with_dc=True, proj_type='wann', save_to_file=False)
dos_parproj = SK.density_of_states(broadening=0.01, with_Sigma=True, with_dc=True, proj_type='wien2k', save_to_file=False) dos_parproj = SK.density_of_states(broadening=0.01, with_Sigma=True, with_dc=True, proj_type='wien2k', save_to_file=False)
#spaghetti = SK.spaghettis(broadening=0.01, plot_shift=0.0, plot_range=(-1,1), ishell=None, save_to_file=False)
[spaghetti, pAkw, pAkw_orb] = SK.spaghettis(broadening=0.01, plot_shift=0.0, plot_range=(-1,1), shell_list=None, save_to_file=False) [spaghetti, pAkw, pAkw_orb] = SK.spaghettis(broadening=0.01, plot_shift=0.0, plot_range=(-1,1), shell_list=None, save_to_file=False)