Updated benchmark

.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

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

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)

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:

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 <references:references>`.

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`

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 = "[email protected]" },
     { name = "Riccardo De Gennaro", email = "[email protected]" },
@@ -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",
 ]

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]]:

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

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