diff --git a/.readthedocs.yml b/.readthedocs.yml
index 24444978e..2d930ff5f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,6 +5,12 @@
# Required
version: 2
+# Specify the python version
+build:
+ os: "ubuntu-22.04"
+ tools:
+ python: "3.8"
+
# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: docs/conf.py
diff --git a/CITATION.cff b/CITATION.cff
index 826f353e6..2764087a2 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -70,4 +70,4 @@ preferred-citation:
repository-code: https://github.com/epfl-theos/koopmans/
title: koopmans
type: software
-version: 1.0.0rc1
+version: 1.0.0
diff --git a/LICENSE b/LICENSE
index f288702d2..d159169d1 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,622 +1,281 @@
GNU GENERAL PUBLIC LICENSE
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+ Version 2, June 1991
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+ NO WARRANTY
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+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
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+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
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END OF TERMS AND CONDITIONS
@@ -628,15 +287,15 @@ free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
+convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
- This program is free software: you can redistribute it and/or modify
+ This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
+ the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
@@ -644,31 +303,37 @@ the "copyright" line and a pointer to where the full notice is found.
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ , 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
diff --git a/docs/conf.py b/docs/conf.py
index 7d8479118..6b130607a 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -8,8 +8,14 @@
import os
import sys
+from calendar import month_name
+from datetime import date
+import pybtex.plugin
import sphinx_rtd_theme
+from pybtex.style.formatting.plain import Style as PlainStyle
+from pybtex.style.formatting.unsrt import Style as UnsrtStyle
+from pybtex.style.sorting import BaseSortingStyle
from sphinx_pyproject import SphinxConfig
# If extensions (or modules to document with autodoc) are in another directory,
@@ -68,3 +74,33 @@
autodoc_typehints = 'none'
autodoc_mock_imports = ['ase']
numpydoc_show_class_members = False
+
+# -- Chronological bibliography style -----------------------------------------
+
+
+class ChronoSortingStyle(BaseSortingStyle):
+ def sort(self, entries):
+ def get_date(entry):
+ month_lookup = list(month_name)
+ year = int(entry.fields['year'])
+ month = month_lookup.index(entry.fields.get('month', 'January'))
+ return date(year, month, 1)
+ return sorted(entries, key=get_date)
+
+
+class MyChronoStyle(UnsrtStyle):
+ def __init__(self, *args, **kwargs):
+ kwargs.update(sorting_style=ChronoSortingStyle, abbreviate_names=True)
+ return super().__init__(*args, **kwargs)
+
+
+pybtex.plugin.register_plugin('pybtex.style.formatting', 'chrono', MyChronoStyle)
+
+
+class MyAbbrevPlainStyle(PlainStyle):
+ def __init__(self, *args, **kwargs):
+ kwargs.update(abbreviate_names=True)
+ return super().__init__(*args, **kwargs)
+
+
+pybtex.plugin.register_plugin('pybtex.style.formatting', 'plainabbrev', MyAbbrevPlainStyle)
diff --git a/docs/references.rst b/docs/references.rst
index 7d0a0e9f7..c4822858d 100644
--- a/docs/references.rst
+++ b/docs/references.rst
@@ -1,7 +1,76 @@
References
==========
-For publications using Koopmans spectral functionals, please cite :cite:`Borghi2014`, :cite:`Nguyen2018`, and ...
+
+Selected references
+-------------------
+
+In any publication arising from the use of Koopmans functionals and/or the ``koopmans`` code, please cite
+
+.. bibliography::
+ :style: chrono
+ :filter: False
+ :list: bullet
+
+ Linscott2023
+
+Other relevant references include
+
+**Papers introducing Koopmans functionals**
+
+.. bibliography::
+ :style: chrono
+ :filter: False
+ :list: bullet
+
+ Dabo2009
+ Dabo2010
+ Borghi2014
+ Borghi2015
+
+**Linear-response formalism**
+
+.. bibliography::
+ :style: chrono
+ :filter: False
+ :list: bullet
+
+ Colonna2018
+
+**Application to molecules**
+
+.. bibliography::
+ :style: chrono
+ :filter: False
+ :list: bullet
+
+ Dabo2013
+ Nguyen2015
+ Nguyen2016
+ Colonna2019
+
+**Application to solids**
+
+.. bibliography::
+ :style: chrono
+ :filter: False
+ :list: bullet
+
+ Nguyen2018
+ Colonna2022
+ DeGennaro2022
+
+**Connection with many-body formulations**
+
+.. bibliography::
+ :style: chrono
+ :filter: False
+ :list: bullet
+
+ Ferretti2014
+
+All references
+--------------
.. bibliography::
- :style: plain
+ :style: plainabbrev
:all:
diff --git a/docs/theory.rst b/docs/theory.rst
index 1ff682ab9..8ab527258 100644
--- a/docs/theory.rst
+++ b/docs/theory.rst
@@ -9,5 +9,6 @@ This section contains a brief introduction to Koopmans functionals.
theory/ingredients
theory/workflows
theory/limitations
+ theory/related_methods
For more details, refer to our various :ref:`publications `.
diff --git a/docs/theory/related_methods.rst b/docs/theory/related_methods.rst
new file mode 100644
index 000000000..439570e44
--- /dev/null
+++ b/docs/theory/related_methods.rst
@@ -0,0 +1,10 @@
+Related methods
+===============
+
+Koopmans functionals have resonance with various methods developed by other groups. These include...
+
+- the Wannier transition-state method of Anisimov and Kozhevnikov :cite:`Anisimov2005`
+- the optimally-tuned range-separated hybrid functionals of Kronik, Neaton, and others :cite:`Kronik2012,Wing2021`
+- the localized orbital scaled correction of Yang and others :cite:`Li2018`
+- the ensemble DFT method of Kreisler, Kronik and others :cite:`Kraisler2013`
+- the Koopmans-Wannier method of Wang and others :cite:`Ma2016`
diff --git a/pyproject.toml b/pyproject.toml
index b838722ca..38539dfd8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ name = "koopmans"
version = "1.0.1"
description = "Koopmans spectral functional calculations with python and Quantum ESPRESSO"
readme = "README_pypi.rst"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
authors = [
{ name = "Edward Linscott", email = "edward.linscott@epfl.ch" },
{ name = "Riccardo De Gennaro", email = "riccardo.degennaro@epfl.ch" },
@@ -13,7 +13,6 @@ classifiers = [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
"Programming Language :: Python :: 3",
- "Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
@@ -31,7 +30,7 @@ dependencies = [
"pybtex>=0.24",
"spglib>=1.9",
"upf-to-json>=0.9.5",
- "ase-koopmans==0.1.1",
+ "ase-koopmans==0.1.4",
"scikit-learn>=1.0",
"deepdiff>=5.8.1",
]
diff --git a/quantum_espresso/q-e b/quantum_espresso/q-e
index 564a7b486..b4c5e8dee 160000
--- a/quantum_espresso/q-e
+++ b/quantum_espresso/q-e
@@ -1 +1 @@
-Subproject commit 564a7b486665e8dd0223d6e514b84195d1a96c10
+Subproject commit b4c5e8deeb7d1863e7553a87b45f8d22c21926a5
diff --git a/src/koopmans/bands.py b/src/koopmans/bands.py
index bd0a03110..0a79b9c18 100644
--- a/src/koopmans/bands.py
+++ b/src/koopmans/bands.py
@@ -161,7 +161,7 @@ def _check_array_shape_match(self, array, array_name):
f'array of length {len(array)}'
for i, (subarray, n_bands) in enumerate(zip(array, self.n_bands)):
assert len(subarray) == n_bands, f'Bands.{array_name}[{i}] must be length {n_bands} but you provided an ' \
- f'array with length {len(subarray)}'
+ f'array with length {len(subarray)}. The file_alpharef files should reflect the number of states in the supercell.'
@property
def filling(self) -> List[List[bool]]:
diff --git a/src/koopmans/calculators/_ph.py b/src/koopmans/calculators/_ph.py
index 9b19a1dd2..17388cf60 100644
--- a/src/koopmans/calculators/_ph.py
+++ b/src/koopmans/calculators/_ph.py
@@ -14,7 +14,7 @@
from ase import Atoms
from ase.calculators.espresso import EspressoPh
-from koopmans.commands import ParallelCommand
+from koopmans.commands import ParallelCommand, Command
from koopmans.settings import PhSettingsDict
from ._utils import CalculatorABC, CalculatorExt
@@ -42,7 +42,11 @@ def is_complete(self):
def _calculate(self):
super()._calculate()
- self.read_dynG()
+ if self.parameters.trans:
+ self.read_dynG()
+ else:
+ self.read_stdout()
+
def read_dynG(self):
with open(self.parameters.fildyn, 'r') as fd:
@@ -52,3 +56,12 @@ def read_dynG(self):
k = [x.strip() for x in flines].index('Effective Charges E-U: Z_{alpha}{s,beta}')
epsilon = np.array([x.split() for x in flines[i + 2: k - 1]], dtype=float)
self.results['dielectric tensor'] = epsilon
+
+ def read_stdout(self):
+ path=f'{self.prefix}{self.ext_out}'
+ with open(path, 'r') as fd:
+ flines = fd.readlines()
+
+ i = [x.strip() for x in flines].index('Dielectric constant in cartesian axis')
+ epsilon = np.array([x.split()[1:4] for x in flines[i + 2: i + 5]], dtype=float)
+ self.results['dielectric tensor'] = epsilon
diff --git a/src/koopmans/kpoints.py b/src/koopmans/kpoints.py
index 962d8d286..a49744389 100644
--- a/src/koopmans/kpoints.py
+++ b/src/koopmans/kpoints.py
@@ -26,6 +26,9 @@ class Kpoints:
offset : List[int]
a list of three integers, either zero or one. If one, the regular k-point grid is offset by half a grid step
in that dimension
+ offset_nscf : Union[List[Union[int, float]]], int, float]
+ a list of three numbers, within the interval (-1, 1].
+ It has the same meaning of offset, but it is applied only to the grid of PWnscf calculations. Additionally it allows to provide explicitly any fractional offset.
path : ase.dft.kpoints.BandPath
an ASE ``BandPath`` object specifying the k-path as defined by the special points of the Bravais
lattice
@@ -35,10 +38,12 @@ class Kpoints:
_grid: Optional[List[int]]
_offset: Optional[List[int]]
+ _offset_nscf: Optional[Union[List[Union[int, float]], int, float]]
_path: Optional[BandPath]
gamma_only: bool
def __init__(self, grid: Optional[List[int]] = [1, 1, 1], offset: Optional[List[int]] = [0, 0, 0],
+ offset_nscf: Optional[Union[List[Union[int, float]], int, float]] = None,
path: Optional[Union[str, BandPath]] = None, gamma_only: bool = False, cell: Optional[Cell] = None,
density: float = 10.0):
"""
@@ -57,9 +62,11 @@ def __init__(self, grid: Optional[List[int]] = [1, 1, 1], offset: Optional[List[
raise ValueError(f'gamma_only = {gamma_only} and grid != None are incompatible')
self.grid = None
self.offset = [0, 0, 0]
+ self.offset_nscf = None
else:
self.grid = grid
self.offset = offset
+ self.offset_nscf = offset_nscf
self.set_path(path, cell, density)
@@ -100,6 +107,28 @@ def offset(self, value: Optional[List[int]]):
raise ValueError('"offset" must only contain either 0 or 1s')
self._offset = value
+ @property
+ def offset_nscf(self) -> Optional[Union[List[Union[int, float]], int, float]]:
+ return self._offset_nscf
+
+ @offset_nscf.setter
+ def offset_nscf(self, value: Optional[Union[List[Union[int, float]], int, float]]):
+ if isinstance(value, list):
+ if len(value) != 3:
+ raise ValueError('"offset" must be a list of three numbers')
+ if any([k <= -1 or k > 1 for k in value]):
+ raise ValueError('"offset_nscf" elements take values within (-1, 1]')
+ if all([k - int(k) == 0 for k in value]):
+ self._offset_nscf = [int(k) for k in value]
+ else:
+ self._offset_nscf = value
+ elif isinstance(value, (int, float)):
+ self._offset_nscf = int(value) if value - int(value) == 0 else value
+ elif value is None:
+ self._offset_nscf = value
+ else:
+ raise ValueError('"offset_nscf" must be a number or a list of three numbers')
+
@property
def path(self) -> Optional[BandPath]:
return self._path
diff --git a/src/koopmans/references.bib b/src/koopmans/references.bib
index a09f2fa41..98275e3f4 100644
--- a/src/koopmans/references.bib
+++ b/src/koopmans/references.bib
@@ -1,16 +1,31 @@
+@article{Anisimov2005,
+ title = {Transition State Method and {{Wannier}} Functions},
+ author = {Anisimov, V. I. and Kozhevnikov, A. V.},
+ year = {2005},
+ month = aug,
+ journal = {Phys. Rev. B},
+ volume = {72},
+ number = {7},
+ pages = {075125},
+ publisher = {{American Physical Society}},
+ doi = {10.1103/PhysRevB.72.075125},
+ urldate = {2020-12-13},
+ abstract = {We propose a computational scheme for materials where standard local density approximation (LDA) fails to produce a satisfactory description of excitation energies. The method uses Slater's ``transition state'' approximation and Wannier functions basis set. We define a correction to LDA functional in such a way that its variation produces one-electron energies for Wannier functions equal to the energies obtained in transition state constrained LDA calculations. In the result eigenvalues of the proposed functional could be interpreted as excitation energies of the system under consideration. The method was applied to MgO, Si, NiO, and BaBiO3 and gave an improved agreement with experimental data of energy gap values comparing with LDA.}
+}
@article{Baroni2001,
title = {Phonons and Related Crystal Properties from Density-Functional Perturbation Theory},
author = {Baroni, Stefano and {de Gironcoli}, Stefano and Dal Corso, Andrea and Giannozzi, Paolo},
year = {2001},
month = jul,
- journal = {Reviews of Modern Physics},
+ journal = {Rev. Mod. Phys.},
volume = {73},
number = {2},
pages = {515--562},
publisher = {{American Physical Society}},
issn = {0034-6861},
- doi = {10.1103/RevModPhys.73.515}
+ doi = {10.1103/RevModPhys.73.515},
+ urldate = {2018-11-06}
}
@article{Borghi2014,
@@ -18,13 +33,14 @@ @article{Borghi2014
author = {Borghi, Giovanni and Ferretti, Andrea and Nguyen, Ngoc Linh and Dabo, Ismaila and Marzari, Nicola},
year = {2014},
month = aug,
- journal = {Physical Review B},
+ journal = {Phys. Rev. B},
volume = {90},
number = {7},
pages = {075135},
publisher = {{American Physical Society}},
issn = {1098-0121},
- doi = {10.1103/PhysRevB.90.075135}
+ doi = {10.1103/PhysRevB.90.075135},
+ urldate = {2017-11-23}
}
@article{Borghi2015,
@@ -32,13 +48,15 @@ @article{Borghi2015
author = {Borghi, Giovanni and Park, Cheol Hwan and Nguyen, Ngoc Linh and Ferretti, Andrea and Marzari, Nicola},
year = {2015},
month = apr,
- journal = {Physical Review B - Condensed Matter and Materials Physics},
+ journal = {Phys. Rev. B},
volume = {91},
number = {15},
pages = {155112},
publisher = {{American Physical Society}},
issn = {1550235X},
- doi = {10.1103/PhysRevB.91.155112}
+ doi = {10.1103/PhysRevB.91.155112},
+ urldate = {2020-02-20},
+ abstract = {Orbital-density-dependent functionals, such as the Perdew-Zunger or the Koopmans-compliant functionals, are used to remove unphysical self-interaction energies and to restore missing piece-wise linearity in approximate formulations of density-functional theory (DFT). At variance with functionals of the total density, orbital-density-dependent functionals are typically not invariant with respect to unitary transformations of the occupied states. Such additional degrees of freedom require an extension of established approaches for direct minimization that preserve their numerical robustness and efficiency, and make it possible to apply these advanced electronic-structure functionals to large or complex systems. In this work we adapt the ensemble-DFT algorithm [N. Marzari, D. Vanderbilt, and M. C. Payne, Phys. Rev. Lett. 79, 1337 (1997)PRLTAO0031-900710.1103/PhysRevLett.79.1337] to the case of orbital-density-dependent functionals, partitioning the variational problem into a nested loop of (i) minimizations with respect to unitary transformations at a fixed orbital manifold, that lead to a projected, unitary-covariant functional of the orbitals only that enforces the Pederson condition and (ii) variational optimization of the orbital manifold for this projected functional. We discuss in detail both general and functional-dependent trends and suggest a procedure to efficiently exploit the combination of the different minimization strategies. The overall formulation allows for a stable, robust, and efficient algorithm, yielding great improvements over conventional techniques.}
}
@article{Colonna2018,
@@ -46,16 +64,15 @@ @article{Colonna2018
author = {Colonna, Nicola and Nguyen, Ngoc Linh and Ferretti, Andrea and Marzari, Nicola},
year = {2018},
month = may,
- journal = {Journal of Chemical Theory and Computation},
+ journal = {J. Chem. Theory Comput.},
volume = {14},
number = {5},
- eprint = {1711.04485},
- eprinttype = {arxiv},
pages = {2549--2557},
publisher = {{American Chemical Society}},
issn = {15499626},
doi = {10.1021/acs.jctc.7b01116},
- archiveprefix = {arXiv}
+ urldate = {2019-11-14},
+ abstract = {Electronic-structure functionals that include screening effects, such as Hubbard or Koopmans' functionals, are required to describe the response of a system to the fractional addition or removal of an electron from an orbital or a manifold. Here, we present a general method to incorporate screening based on linear-response theory, and we apply it to the case of orbital-by-orbital screening of Koopmans' functionals. We illustrate the importance of such generalization when dealing with challenging systems containing orbitals with very different chemical character, also highlighting the simple dependence of the screening on the localization of the orbitals. We choose a set of 46 transition-metal complexes for which experimental data and accurate many-body perturbation theory calculations are available. When compared to experiment, results for ionization potentials show a very good performance, with a mean absolute error of 0.2 eV, comparable to the most accurate many-body perturbation theory approaches. These results reiterate the role of Koopmans-compliant functionals as simple and accurate quasiparticle approximations to the exact spectral functional, bypassing diagrammatic expansions and relying only on the physics of the local density or generalized-gradient approximation.}
}
@article{Colonna2019,
@@ -63,13 +80,15 @@ @article{Colonna2019
author = {Colonna, Nicola and Nguyen, Ngoc Linh and Ferretti, Andrea and Marzari, Nicola},
year = {2019},
month = mar,
- journal = {Journal of Chemical Theory and Computation},
+ journal = {J. Chem. Theory Comput.},
volume = {15},
number = {3},
pages = {1905--1914},
publisher = {{American Chemical Society}},
issn = {1549-9618},
- doi = {10.1021/acs.jctc.8b00976}
+ doi = {10.1021/acs.jctc.8b00976},
+ urldate = {2019-03-21},
+ abstract = {Koopmans-compliant (KC) functionals have been shown to provide accurate spectral properties through a generalized condition of piecewise linearity of the total energy as a function of the fractional addition/removal of an electron to/from any orbital. We analyze the performance of different KC functionals on a large and standardized set of 100 molecules, the GW100 test set, comparing vertical ionization potentials (taken as opposite of the orbital energies) to those obtained from accurate quantum chemistry methods, and to experimental results. We find excellent agreement, with a mean absolute error of 0.20 eV for the KIPZ functional on the first ionization potential, which is state-of-the-art for both density functional theory (DFT)-based calculations and many-body perturbation theory. We highlight similarities and differences between KC functionals and other electronic-structure approaches, such as dielectric-dependent hybrid functionals and Green's function methods, both from a theoretical and from a pr...}
}
@article{Colonna2022,
@@ -77,9 +96,11 @@ @article{Colonna2022
author = {Colonna, Nicola and Gennaro, Riccardo De and Linscott, Edward and Marzari, Nicola},
year = {2022},
month = aug,
- journal = {Journal of Chemical Theory and Computation},
+ journal = {J. Chem. Theory Comput.},
publisher = {{American Chemical Society}},
doi = {10.1021/acs.jctc.2c00161},
+ urldate = {2022-08-09},
+ abstract = {Koopmans spectral functionals aim to describe simultaneously ground-state properties and charged excitations of atoms, molecules, nanostructures, and periodic crystals. This is achieved by augmenting standard density functionals with simple but physically motivated orbital-density-dependent corrections. These corrections act on a set of localized orbitals that, in periodic systems, resemble maximally localized Wannier functions. At variance with the original, direct supercell implementation (Phys. Rev. X 2018, 8, 021051), we discuss here (i) the complex but efficient formalism required for a periodic boundary code using explicit Brillouin zone sampling and (ii) the calculation of the screened Koopmans corrections with density functional perturbation theory. In addition to delivering improved scaling with system size, the present development makes the calculation of band structures with Koopmans functionals straightforward. The implementation in the open-source Quantum ESPRESSO distribution and the application to prototypical insulating and semiconducting systems are presented and discussed.},
copyright = {\textcopyright{} 2022 American Chemical Society},
langid = {english}
}
@@ -90,8 +111,8 @@ @misc{Dabo2009
year = {2009},
month = jan,
eprint = {0901.2637},
- eprinttype = {arxiv},
- archiveprefix = {arXiv}
+ abstract = {In effective single-electron theories, self-interaction manifests itself through the unphysical dependence of the energy of an electronic state as a function of its occupation, which results in important deviations from the ideal Koopmans trend and strongly affects the accuracy of electronic-structure predictions. Here, we study the non-Koopmans behavior of local and semilocal density-functional theory (DFT) total energy methods as a means to quantify and to correct self-interaction errors. We introduce a non-Koopmans self-interaction correction that generalizes the Perdew-Zunger scheme, and demonstrate its considerably improved performance in correcting the deficiencies of DFT approximations for self-interaction problems of fundamental and practical relevance.},
+ archiveprefix = {arxiv}
}
@article{Dabo2010,
@@ -99,13 +120,14 @@ @article{Dabo2010
author = {Dabo, Ismaila and Ferretti, Andrea and Poilvert, Nicolas and Li, Yanli and Marzari, Nicola and Cococcioni, Matteo},
year = {2010},
month = sep,
- journal = {Physical Review B},
+ journal = {Phys. Rev. B},
volume = {82},
number = {11},
pages = {115121},
publisher = {{American Physical Society}},
issn = {1098-0121},
- doi = {10.1103/PhysRevB.82.115121}
+ doi = {10.1103/PhysRevB.82.115121},
+ urldate = {2017-11-23}
}
@article{Dabo2013,
@@ -113,15 +135,14 @@ @article{Dabo2013
author = {Dabo, Ismaila and Ferretti, Andrea and Park, Cheol Hwan and Poilvert, Nicolas and Li, Yanli and Cococcioni, Matteo and Marzari, Nicola},
year = {2013},
month = jan,
- journal = {Physical Chemistry Chemical Physics},
+ journal = {Phys. Chem. Chem. Phys.},
volume = {15},
number = {2},
- eprint = {1210.7973},
- eprinttype = {arxiv},
pages = {685--695},
issn = {14639076},
doi = {10.1039/c2cp43491a},
- archiveprefix = {arXiv}
+ urldate = {2019-11-14},
+ abstract = {Accurate and efficient approaches to predict the optical properties of organic semiconducting compounds could accelerate the search for efficient organic photovoltaic materials. Nevertheless, predicting the optical properties of organic semiconductors has been plagued by the inaccuracy or computational cost of conventional first-principles calculations. In this work, we demonstrate that orbital-dependent density-functional theory based upon Koopmans' condition [Phys. Rev. B, 2010, 82, 115121] is apt for describing donor and acceptor levels for a wide variety of organic molecules, clusters, and oligomers within a few tenths of an electron-volt relative to experiment, which is comparable to the predictive performance of many-body perturbation theory methods at a fraction of the computational cost. \textcopyright{} the Owner Societies 2013.}
}
@article{DeGennaro2022,
@@ -136,6 +157,8 @@ @article{DeGennaro2022
pages = {035106},
publisher = {{American Physical Society}},
doi = {10.1103/PhysRevB.106.035106},
+ urldate = {2022-07-08},
+ abstract = {Koopmans-compliant functionals provide an orbital-density-dependent framework for an accurate evaluation of spectral properties; they are obtained by imposing a generalized piecewise-linearity condition on the total energy of the system with respect to the occupation of any orbital. In crystalline materials, due to the orbital-density-dependent nature of the functionals, minimization of the total energy to a ground state provides a set of minimizing variational orbitals that are localized and thus break the periodicity of the underlying lattice. Despite this, we show that Bloch symmetry can be preserved and it is possible to describe the electronic states with a band-structure picture, thanks to the Wannier-like character of the variational orbitals. We also present a method to unfold and interpolate the electronic bands from supercell ({$\Gamma$}-point) calculations, which enables us to calculate full band structures with Koopmans-compliant functionals. The results obtained for a set of benchmark semiconductors and insulators show very good agreement with state-of-the-art many-body perturbation theory and experiments, underscoring the reliability of these spectral functionals in predicting band structures.},
copyright = {All rights reserved}
}
@@ -144,13 +167,14 @@ @article{Ferretti2014
author = {Ferretti, Andrea and Dabo, Ismaila and Cococcioni, Matteo and Marzari, Nicola},
year = {2014},
month = may,
- journal = {Physical Review B},
+ journal = {Phys. Rev. B},
volume = {89},
number = {19},
pages = {195134},
publisher = {{American Physical Society}},
issn = {1098-0121},
- doi = {10.1103/PhysRevB.89.195134}
+ doi = {10.1103/PhysRevB.89.195134},
+ urldate = {2019-03-23}
}
@article{Hamann2013,
@@ -158,13 +182,47 @@ @article{Hamann2013
author = {Hamann, D. R.},
year = {2013},
month = aug,
- journal = {Physical Review B - Condensed Matter and Materials Physics},
+ journal = {Phys. Rev. B},
volume = {88},
number = {8},
pages = {085117},
publisher = {{American Physical Society}},
issn = {10980121},
- doi = {10.1103/PhysRevB.88.085117}
+ doi = {10.1103/PhysRevB.88.085117},
+ urldate = {2020-06-23},
+ abstract = {Fully nonlocal two-projector norm-conserving pseudopotentials are shown to be compatible with a systematic approach to the optimization of convergence with the size of the plane-wave basis. A reformulation of the optimization is developed, including the ability to apply it to positive-energy atomic scattering states and to enforce greater continuity in the pseudopotential. The generalization of norm conservation to multiple projectors is reviewed and recast for the present purposes. Comparisons among the results of all-electron and one- and two-projector norm-conserving pseudopotential calculations of lattice constants and bulk moduli are made for a group of solids chosen to represent a variety of types of bonding and a sampling of the periodic table. \textcopyright{} 2013 American Physical Society.}
+}
+
+@article{Kraisler2013,
+ title = {Piecewise {{Linearity}} of {{Approximate Density Functionals Revisited}}: {{Implications}} for {{Frontier Orbital Energies}}},
+ shorttitle = {Piecewise {{Linearity}} of {{Approximate Density Functionals Revisited}}},
+ author = {Kraisler, Eli and Kronik, Leeor},
+ year = {2013},
+ month = mar,
+ journal = {Phys. Rev. Lett.},
+ volume = {110},
+ number = {12},
+ pages = {126403},
+ publisher = {{American Physical Society}},
+ doi = {10.1103/PhysRevLett.110.126403},
+ urldate = {2022-09-28},
+ abstract = {In the exact Kohn-Sham density-functional theory, the total energy versus the number of electrons is a series of linear segments between integer points. However, commonly used approximate density functionals produce total energies that do not exhibit this piecewise-linear behavior. As a result, the ionization potential theorem, equating the highest occupied eigenvalue with the ionization potential, is grossly disobeyed. Here, we show that, contrary to conventional wisdom, most of the required piecewise linearity of an arbitrary approximate density functional can be restored by careful consideration of the ensemble generalization of density-functional theory. Furthermore, the resulting formulation introduces the desired derivative discontinuity to any approximate exchange-correlation functional, even one that is explicitly density dependent. This opens the door to calculations of the ionization potential and electron affinity, even without explicit electron removal or addition. All these advances are achieved while neither introducing empiricism nor changing the underlying functional form. The power of the approach is demonstrated on benchmark systems using the local density approximation as an illustrative example.}
+}
+
+@article{Kronik2012,
+ title = {Excitation {{Gaps}} of {{Finite-Sized Systems}} from {{Optimally Tuned Range-Separated Hybrid Functionals}}},
+ author = {Kronik, Leeor and Stein, Tamar and {Refaely-Abramson}, Sivan and Baer, Roi},
+ year = {2012},
+ month = may,
+ journal = {J. Chem. Theory Comput.},
+ volume = {8},
+ number = {5},
+ pages = {1515--1531},
+ publisher = {{American Chemical Society}},
+ issn = {1549-9618},
+ doi = {10.1021/ct2009363},
+ urldate = {2022-10-17},
+ abstract = {Excitation gaps are of considerable significance in electronic structure theory. Two different gaps are of particular interest. The fundamental gap is defined by charged excitations, as the difference between the first ionization potential and the first electron affinity. The optical gap is defined by a neutral excitation, as the difference between the energies of the lowest dipole-allowed excited state and the ground state. Within many-body perturbation theory, the fundamental gap is the difference between the corresponding lowest quasi-hole and quasi-electron excitation energies, and the optical gap is addressed by including the interaction between a quasi-electron and a quasi-hole. A long-standing challenge has been the attainment of a similar description within density functional theory (DFT), with much debate on whether this is an achievable goal even in principle. Recently, we have constructed and applied a new approach to this problem. Anchored in the rigorous theoretical framework of the generalized Kohn\textendash Sham equation, our method is based on a range-split hybrid functional that uses exact long-range exchange. Its main novel feature is that the range-splitting parameter is not a universal constant but rather is determined from first principles, per system, based on satisfaction of the ionization potential theorem. For finite-sized objects, this DFT approach mimics successfully, to the best of our knowledge for the first time, the quasi-particle picture of many-body theory. Specifically, it allows for the extraction of both the fundamental and the optical gap from one underlying functional, based on the HOMO\textendash LUMO gap of a ground-state DFT calculation and the lowest excitation energy of a linear-response time-dependent DFT calculation, respectively. In particular, it produces the correct optical gap for the difficult case of charge-transfer and charge-transfer-like scenarios, where conventional functionals are known to fail. In this perspective, we overview the formal and practical challenges associated with gap calculations, explain our new approach and how it overcomes previous difficulties, and survey its application to a variety of systems.}
}
@article{Lejaeghere2016,
@@ -177,7 +235,53 @@ @article{Lejaeghere2016
number = {6280},
pages = {aad3000},
publisher = {{American Association for the Advancement of Science}},
- doi = {10.1126/science.aad3000}
+ doi = {10.1126/science.aad3000},
+ urldate = {2022-02-17}
+}
+
+@article{Li2018,
+ title = {Localized Orbital Scaling Correction for Systematic Elimination of Delocalization Error in Density Functional Approximations},
+ author = {Li, Chen and Zheng, Xiao and Su, Neil Qiang and Yang, Weitao},
+ year = {2018},
+ journal = {Natl. Sci. Rev.},
+ volume = {5},
+ pages = {203--215},
+ url = {https://academic.oup.com/nsr/article/5/2/203/4104965},
+ urldate = {2020-04-04}
+}
+
+@misc{Linscott2023,
+ title = {Koopmans: An Open-Source Package for Accurately and Efficiently Predicting Spectral Properties with {{Koopmans}} Functionals},
+ shorttitle = {Koopmans},
+ author = {Linscott, Edward and Colonna, Nicola and De Gennaro, Riccardo and Nguyen, Ngoc Linh and Borghi, Giovanni and Ferretti, Andrea and Dabo, Ismaila and Marzari, Nicola},
+ year = {2023},
+ month = feb,
+ number = {2302.07759},
+ eprint = {2302.07759},
+ primaryclass = {cond-mat, physics:physics},
+ publisher = {{arXiv}},
+ abstract = {Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional formulation. These functionals address two fundamental issues with density functional theory (DFT). First, while Kohn-Sham eigenvalues can loosely mirror experimental quasiparticle energies, they are not meant to reproduce excitation energies and there is formally no connection between the two (except for the HOMO for the exact functional). Second, (semi-)local DFT deviates from the expected piecewise linear behavior of the energy as a function of the total number of electrons. This can make eigenvalues an even poorer proxy for quasiparticle energies and, together with the absence of the exchange-correlation derivative discontinuity, contributes to DFT's underestimation of band gaps. By enforcing a generalized piecewise linearity condition to the entire electronic manifold, Koopmans functionals yield molecular orbital energies and solid-state band structures with comparable accuracy to many-body perturbation theory but at greatly reduced computational cost and preserving a functional formulation. This paper introduces "koopmans", an open-source package that contains all of the code and workflows needed to perform Koopmans functional calculations without requiring expert knowledge. The theory and algorithms behind Koopmans functionals are summarized, and it is shown how one can easily use the koopmans package to obtain reliable spectral properties of molecules and materials.},
+ archiveprefix = {arxiv},
+ copyright = {All rights reserved},
+ keywords = {Condensed Matter - Materials Science,Physics - Chemical Physics,Physics - Computational Physics}
+}
+
+@article{Ma2016,
+ title = {Using {{Wannier}} Functions to Improve Solid Band Gap Predictions in Density Functional Theory},
+ author = {Ma, Jie and Wang, Lin-Wang},
+ year = {2016},
+ month = apr,
+ journal = {Sci. Rep.},
+ volume = {6},
+ number = {1},
+ pages = {24924},
+ publisher = {{Nature Publishing Group}},
+ issn = {2045-2322},
+ doi = {10.1038/srep24924},
+ urldate = {2020-11-25},
+ abstract = {Enforcing a straight-line condition of the total energy upon removal/addition of fractional electrons on eigen states has been successfully applied to atoms and molecules for calculating ionization potentials and electron affinities, but fails for solids due to the extended nature of the eigen orbitals. Here we have extended the straight-line condition to the removal/addition of fractional electrons on Wannier functions constructed within the occupied/unoccupied subspaces. It removes the self-interaction energies of those Wannier functions, and yields accurate band gaps for solids compared to experiments. It does not have any adjustable parameters and the computational cost is at the DFT level. This method can also work for molecules, providing eigen energies in good agreement with experimental ionization potentials and electron affinities. Our approach can be viewed as an alternative approach of the standard LDA+U procedure.},
+ copyright = {2016 The Author(s)},
+ langid = {english}
}
@article{Marzari2012,
@@ -185,13 +289,14 @@ @article{Marzari2012
author = {Marzari, Nicola and Mostofi, Arash A. and Yates, Jonathan R. and Souza, Ivo and Vanderbilt, David},
year = {2012},
month = oct,
- journal = {Reviews of Modern Physics},
+ journal = {Rev. Mod. Phys.},
volume = {84},
number = {4},
pages = {1419--1475},
publisher = {{American Physical Society}},
issn = {0034-6861},
- doi = {10.1103/RevModPhys.84.1419}
+ doi = {10.1103/RevModPhys.84.1419},
+ urldate = {2018-08-29}
}
@article{Nattino2019,
@@ -202,14 +307,26 @@ @article{Nattino2019
journal = {J. Chem. Theory Comput.},
volume = {15},
number = {11},
- eprint = {1906.00822},
- eprinttype = {arxiv},
pages = {6313--6322},
- publisher = {{American Chemical Society}},
issn = {15499626},
doi = {10.1021/acs.jctc.9b00552},
- archiveprefix = {arXiv},
- pmid = {31580667}
+ urldate = {2020-06-18},
+ abstract = {Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densities are too inaccurate. Here, an alternative approach is presented, in which an embedding environment is used to stabilize the anion in a bound configuration. Similar to the HF case, when computing total energies at the DFT level on these corrected densities, electron affinities in very good agreement with experiments can be recovered. The effect of the environment can be evaluated and removed by an extrapolation of the results to the limit of vanishing embedding. Apart from the definition of the domain of the embedding potential, the approach is free from parameters and it can be easily applied to DFT calculations with delocalized basis sets, e.g., plane waves, for which alternative approaches are either not viable or more computationally demanding. The proposed extrapolation strategy can be thus applied also to extended systems, as often studied in condensed-matter physics and materials science, and we illustrate how the embedding environment can be exploited to determine the energy of an adsorbing anion, here a chloride ion on a metal surface, whose charge configuration would be incorrectly predicted by standard density functionals.}
+}
+
+@article{Nguyen2015,
+ title = {First-{{Principles Photoemission Spectroscopy}} and {{Orbital Tomography}} in {{Molecules}} from {{Koopmans-Compliant Functionals}}},
+ author = {Nguyen, Ngoc Linh and Borghi, Giovanni and Ferretti, Andrea and Dabo, Ismaila and Marzari, Nicola},
+ year = {2015},
+ month = apr,
+ journal = {Phys. Rev. Lett.},
+ volume = {114},
+ number = {16},
+ pages = {166405},
+ publisher = {{American Physical Society}},
+ doi = {10.1103/PhysRevLett.114.166405},
+ urldate = {2021-06-16},
+ abstract = {The determination of spectral properties from first principles can provide powerful connections between microscopic theoretical predictions and experimental data, but requires complex electronic-structure formulations that fall outside the domain of applicability of common approaches, such as density-functional theory. We show here that Koopmans-compliant functionals, constructed to enforce piecewise linearity and the correct discontinuity derivative in energy functionals with respect to fractional occupation\textemdash i.e., with respect to charged excitations\textemdash provide molecular photoemission spectra and momentum maps of Dyson orbitals that are in excellent agreement with experimental ultraviolet photoemission spectroscopy and orbital tomography data. These results highlight the role of Koopmans-compliant functionals as accurate and inexpensive quasiparticle approximations to the spectral potential.}
}
@article{Nguyen2016,
@@ -217,13 +334,15 @@ @article{Nguyen2016
author = {Nguyen, Ngoc Linh and Borghi, Giovanni and Ferretti, Andrea and Marzari, Nicola},
year = {2016},
month = aug,
- journal = {Journal of Chemical Theory and Computation},
+ journal = {J. Chem. Theory Comput.},
volume = {12},
number = {8},
pages = {3948--3958},
publisher = {{American Chemical Society}},
issn = {15499626},
- doi = {10.1021/acs.jctc.6b00145}
+ doi = {10.1021/acs.jctc.6b00145},
+ urldate = {2020-04-20},
+ abstract = {The need to interpret ultraviolet photoemission data strongly motivates the refinement of first-principles techniques that are able to accurately predict spectral properties. In this work, we employ Koopmans-compliant functionals, constructed to enforce piecewise linearity in approximate density functionals, to calculate the structural and electronic properties of DNA and RNA nucleobases. Our results show that not only ionization potentials and electron affinities are accurately predicted with mean absolute errors of {$<