diff --git a/src/koopmans/calculators/_calculator.py b/src/koopmans/calculators/_calculator.py index d8ef2cb0d..11289854a 100644 --- a/src/koopmans/calculators/_calculator.py +++ b/src/koopmans/calculators/_calculator.py @@ -24,8 +24,9 @@ class ExtendedCalc(CalculatorExt, ASECalc, CalculatorABC): import os from abc import ABC, abstractmethod, abstractproperty from pathlib import Path -from typing import (Any, Dict, Generic, List, Optional, Tuple, Type, TypeVar, - Union) +from typing import (TYPE_CHECKING, Any, Dict, Generic, List, Optional, Tuple, + Type, TypeVar, Union) +from uuid import UUID, uuid4 import ase.io as ase_io import numpy as np @@ -38,6 +39,9 @@ class ExtendedCalc(CalculatorExt, ASECalc, CalculatorABC): from koopmans import settings, utils from koopmans.files import FilePointer +if TYPE_CHECKING: + from koopmans.workflows import Workflow + def sanitize_filenames(filenames: Union[str, Path, List[str], List[Path]], ext_in: str, ext_out: str) -> List[Path]: # Generic function for sanitizing the input of CalculatorExt.fromfile() @@ -74,8 +78,10 @@ class CalculatorExt(): results: Dict[str, Any] ext_in: str = '' ext_out: str = '' + parent: Workflow | None + uuid: str - def __init__(self, skip_qc: bool = False, **kwargs: Any): + def __init__(self, parent=None, skip_qc: bool = False, **kwargs: Any): # Remove arguments that should not be treated as QE keywords kwargs.pop('directory', None) @@ -87,7 +93,13 @@ def __init__(self, skip_qc: bool = False, **kwargs: Any): self.skip_qc = skip_qc # Prepare a dictionary to store a record of linked files - self.linked_files: Dict[str, Tuple[utils.HasDirectoryAttr | None, Path, bool, bool, bool]] = {} + self.linked_files: Dict[str, Tuple[utils.HasDirectoryInfo | None, Path, bool, bool, bool]] = {} + + # Store the parent workflow + self.parent = parent + + # Generate a unique identifier for this calculation + self.uuid = str(uuid4()) def __repr__(self): entries = [] @@ -129,8 +141,29 @@ def directory(self, value: Path | str | None): return if not isinstance(value, Path): value = Path(value) + if value.is_absolute(): + raise ValueError(f'`{self.__class__.__name__}.directory` must be a relative path') self._directory = value + @property + def absolute_directory(self) -> Path: + assert self.directory is not None + if self.parent is None: + return self.directory.resolve() + path = self.parent.directory / self.directory + + # Recursive through the parents, adding their directories to path (these are all relative paths)... + obj = self.parent + while getattr(obj, 'parent', None): + assert obj.parent is not None + path = obj.parent.directory / path + obj = obj.parent + + # ... until we reach the top-level parent, which should have a base_directory attribute (an absolute path) + if not hasattr(obj, 'base_directory'): + raise AttributeError(f'Expected `{obj.__class__.__name__}` instance to have a `base_directory` attribute') + return obj.base_directory / path + def calculate(self): """Generic function for running a calculator""" @@ -166,7 +199,7 @@ def _fetch_linked_files(self): if src_calc is None: src_filename = src_filename.resolve() else: - src_filename = (src_calc.directory / src_filename).resolve() + src_filename = src_calc.absolute_directory / src_filename dest_filename = self.directory / dest_filename if not src_filename.exists(): @@ -232,9 +265,7 @@ def read_input(self, input_file: Optional[Path] = None): # Load calculator from input file calc: Calculator = ase_io.read(input_file).calc - # Update self based off the input file, first updating self.directory in order to ensure any settings that are - # relative paths are appropriately stored - self.directory = input_file.parent + # Update self based off the input file self.parameters = calc.parameters if isinstance(calc.atoms, Atoms): # Some calculators (e.g. wann2kc) can't reconstruct atoms from an input file @@ -281,7 +312,7 @@ def fromdict(cls: Type[TCalc], dct: Any) -> TCalc: setattr(calc, k.lstrip('_'), v) return calc - def link_file(self, src_calc: utils.HasDirectoryAttr | None, src_filename: Path, dest_filename: Path, symlink: bool = False, + def link_file(self, src_calc: utils.HasDirectoryInfo | None, src_filename: Path, dest_filename: Path, symlink: bool = False, recursive_symlink: bool = False, overwrite: bool = False): if src_filename.is_absolute() and src_calc is not None: raise ValueError(f'`src_filename` in `{self.__class__.__name__}.link_file()` must be a relative path if a ' @@ -359,7 +390,6 @@ def fromfile(cls, filenames: Union[str, Path, List[str], List[Path]]): # Read qe output file for filename in [f for f in sanitized_filenames if f.suffix == cls.ext_out]: - calc.directory = filename.parent calc.prefix = filename.stem try: calc.read_results() @@ -368,7 +398,9 @@ def fromfile(cls, filenames: Union[str, Path, List[str], List[Path]]): pass # Update calc.directory and calc.parameters.prefix - calc.directory = sanitized_filenames[0].parent + assert hasattr(calc, 'parent') + base_directory = Path() if calc.parent is None else calc.parent.base_directory / calc.parent.directory + calc.directory = Path(os.path.relpath(sanitized_filenames[0].parent, base_directory)) calc.prefix = sanitized_filenames[0].stem # Return the new calc object diff --git a/src/koopmans/calculators/_koopmans_cp.py b/src/koopmans/calculators/_koopmans_cp.py index 878459cb9..253284c5f 100644 --- a/src/koopmans/calculators/_koopmans_cp.py +++ b/src/koopmans/calculators/_koopmans_cp.py @@ -519,7 +519,10 @@ def has_empty_states(self, spin: Optional[int] = None) -> bool: return self.parameters.nbnd > nel def nspin1_dummy_calculator(self) -> KoopmansCPCalculator: + self.parent, parent = None, self.parent calc = copy.deepcopy(self) + self.parent = parent + calc.parent = parent calc.prefix += '_nspin1_dummy' calc.parameters.do_outerloop = False calc.parameters.do_outerloop_empty = False @@ -536,7 +539,10 @@ def nspin1_dummy_calculator(self) -> KoopmansCPCalculator: return calc def nspin1_calculator(self) -> KoopmansCPCalculator: + self.parent, parent = None, self.parent calc = copy.deepcopy(self) + calc.parent = parent + self.parent = parent calc.prefix += '_nspin1' calc.parameters.nspin = 1 calc.parameters.nelup = None diff --git a/src/koopmans/files.py b/src/koopmans/files.py index af5084346..e215b34ef 100644 --- a/src/koopmans/files.py +++ b/src/koopmans/files.py @@ -4,8 +4,8 @@ import numpy as np -from koopmans.utils import (HasDirectoryAttr, get_binary_content, get_content, - write_binary_content, write_content) +from koopmans.utils import (HasDirectoryInfo, get_binary_content, get_content, + warn, write_binary_content, write_content) class FilePointer(NamedTuple): @@ -17,17 +17,19 @@ class FilePointer(NamedTuple): to koopmans/AiiDA) and a name (which is the path of the file relative to the parent's directory). """ - parent: HasDirectoryAttr + parent: HasDirectoryInfo name: Path def __repr__(self): - assert self.parent.directory is not None - relpath: str = os.path.relpath(self.parent.directory, Path.cwd()) - return f'FilePointer({relpath}/{self.name})' + assert self.parent.absolute_directory is not None + return f'FilePointer({self.parent.absolute_directory}/{self.name})' - def aspath(self): - assert self.parent.directory is not None - return self.parent.directory / self.name + def aspath(self, absolute: bool = True) -> Path: + if absolute: + assert self.parent.absolute_directory is not None + return self.parent.absolute_directory / self.name + else: + return self.name def copy(self, dst: Path, binary=False): if binary: @@ -56,7 +58,8 @@ def read(self, binary: bool = False, numpy: bool = False) -> Any: def rglob(self, pattern: str): for f in self.aspath().rglob(pattern): - yield FilePointer(parent=self.parent, name=f.relative_to(self.parent.directory)) + assert self.parent.absolute_directory is not None + yield FilePointer(parent=self.parent, name=f.relative_to(self.parent.absolute_directory)) def is_dir(self): return self.aspath().is_dir() @@ -64,8 +67,28 @@ def is_dir(self): def __eq__(self, other): if not isinstance(other, FilePointer): return False + # Note that we don't check self.parent.absolute_directory return self.parent.directory == other.parent.directory and self.name == other.name + def __reduce__(self): + # We don't want to store the entire parent object in the database; we only need the directory information + abs_dir = self.parent.absolute_directory + dummy_parent = ParentPlaceholder(directory=self.parent.directory, + absolute_directory=self.parent.absolute_directory) + return (FilePointer, (dummy_parent, self.name)) + + +class ParentPlaceholder: + # Move into the test suite? + def __init__(self, directory, absolute_directory): + self.directory = directory + self._absolute_directory = absolute_directory + + @property + def absolute_directory(self): + # This is a property in order to follow the HasDirectoryInfo protocol + return Path(__file__).parents[2] / self._absolute_directory + class AbsolutePath: """ A class that can stand in as a parent in a FilePointer when the file is unattached to a Calculator or Process """ @@ -79,6 +102,10 @@ def __eq__(self, other): return False return self.directory == other.directory + @property + def absolute_directory(self) -> Path | None: + return self.directory + def AbsoluteFilePointer(path: Path | str) -> FilePointer: path = path if isinstance(path, Path) else Path(path) diff --git a/src/koopmans/io/_dill.py b/src/koopmans/io/_dill.py index 9bce71b92..363433d25 100644 --- a/src/koopmans/io/_dill.py +++ b/src/koopmans/io/_dill.py @@ -1,46 +1,18 @@ +import os from pathlib import Path from typing import Any import dill -class PicklerWithRelativePaths(dill.Pickler): - def __init__(self, base_directory, *args, **kwargs): - super().__init__(*args, **kwargs) - self.base_directory = base_directory - - def reducer_override(self, obj): - if isinstance(obj, Path): - return Path, pickle_path(obj, self.base_directory) - else: - return NotImplemented - - -def pickle_path(path: Path, base_directory: Path): - # Convert the path to relative if it's absolute - if path.is_absolute(): - try: - rel_path = path.relative_to(base_directory.resolve()) - except ValueError: - rel_path = path - return (str(rel_path),) - else: - # Return relative paths as-is - return (str(path),) - - def read_pkl(filename: Path | str) -> Any: with open(filename, 'rb') as fd: out = dill.load(fd) return out -def write_pkl(obj: Any, filename: Path | str, base_directory: Path | None = None): +def write_pkl(obj: Any, filename: Path | str): filename = Path(filename) if not isinstance(filename, Path) else filename - if base_directory is None: - base_directory = filename.parent - with open(filename, 'wb') as fd: - pickler = PicklerWithRelativePaths(base_directory, fd) - pickler.dump(obj) + dill.dump(obj, fd) diff --git a/src/koopmans/processes/_process.py b/src/koopmans/processes/_process.py index be809a35b..c0236203c 100644 --- a/src/koopmans/processes/_process.py +++ b/src/koopmans/processes/_process.py @@ -5,7 +5,8 @@ import re from abc import ABC, abstractmethod from pathlib import Path -from typing import Dict, Generic, Tuple, Type, TypeVar +from typing import TYPE_CHECKING, Dict, Generic, Tuple, Type, TypeVar +from uuid import uuid4 import dill import numpy as np @@ -13,6 +14,9 @@ from koopmans import utils +if TYPE_CHECKING: + from koopmans.workflows import Workflow + class IOModel(BaseModel): # BaseModel with an __eq__ method that compares attributes rather than memory addresses @@ -36,7 +40,7 @@ def __eq__(self, other): class Process(ABC, Generic[InputModel, OutputModel]): - __slots__ = ['inputs', '_outputs', 'name', 'directory'] + __slots__ = ['inputs', '_outputs', 'name', 'directory', 'parent', 'uuid', '_base_directory'] def __init__(self, name: str | None = None, **kwargs): self.inputs: InputModel = self.input_model(**kwargs) @@ -48,6 +52,11 @@ def __init__(self, name: str | None = None, **kwargs): else: self.name = name self.directory: Path | None = None + self.parent: Workflow | None = None + self.uuid = str(uuid4()) + self._base_directory: Path | None = None + if self.parent is None: + self.base_directory = Path() def run(self): assert self.directory is not None, 'Process directory must be set before running' @@ -111,3 +120,37 @@ def is_complete(self): if self.directory is None: raise ValueError('Process directory must be set before checking if it is complete') return (self.directory / f'{self.name}_outputs.pkl').exists() + + @property + def base_directory(self) -> Path: + if self.parent is not None: + return self.parent.base_directory + else: + if self._base_directory is None: + raise ValueError(f'{self.__class__.__name__}.base_directory has not been set') + return self._base_directory + + @base_directory.setter + def base_directory(self, value: Path): + if self.parent is not None: + raise ValueError(f'{self.__class__.__name__}.base_directory should not be set for processes with parents') + self._base_directory = value.resolve() + + @property + def absolute_directory(self) -> Path: + assert self.directory is not None + if self.parent is None: + return self.base_directory / self.directory + path = self.parent.directory / self.directory + + # Recursive through the parents, adding their directories to path (these are all relative paths)... + obj = self.parent + while getattr(obj, 'parent', None): + assert obj.parent is not None + path = obj.parent.directory / path + obj = obj.parent + + # ... until we reach the top-level parent, which should have a base_directory attribute (an absolute path) + if not hasattr(obj, 'base_directory'): + raise AttributeError(f'Expected `{obj.__class__.__name__}` instance to have a `base_directory` attribute') + return obj.base_directory / path diff --git a/src/koopmans/processes/bin2xml.py b/src/koopmans/processes/bin2xml.py index d2c65500d..c89b61485 100644 --- a/src/koopmans/processes/bin2xml.py +++ b/src/koopmans/processes/bin2xml.py @@ -29,7 +29,7 @@ class Bin2XMLProcess(CommandLineTool): output_model = Bin2XMLOutput def _pre_run(self): - if not (self.inputs.binary.parent.directory / self.inputs.binary.name).exists(): + if not (self.inputs.binary.parent.absolute_directory / self.inputs.binary.name).exists(): raise FileNotFoundError(f'`{self.inputs.binary}` does not exist') # Load the file diff --git a/src/koopmans/processes/koopmans_cp.py b/src/koopmans/processes/koopmans_cp.py index 132cc0e9b..b0256a8b1 100644 --- a/src/koopmans/processes/koopmans_cp.py +++ b/src/koopmans/processes/koopmans_cp.py @@ -88,6 +88,8 @@ class SwapSpinFilesProcess(Process): output_model = SwapSpinFilesOutputModel def _run(self): + if not self.inputs.read_directory.exists(): + raise FileNotFoundError(f'{self.inputs.read_directory} does not exist') spin_up_files = list(self.inputs.read_directory.rglob('*1.*')) spin_down_files = list(self.inputs.read_directory.rglob('*2.*')) for src in self.inputs.read_directory.rglob('*'): diff --git a/src/koopmans/processes/ui/_process.py b/src/koopmans/processes/ui/_process.py index 557ec2db8..db9547ec7 100644 --- a/src/koopmans/processes/ui/_process.py +++ b/src/koopmans/processes/ui/_process.py @@ -229,7 +229,7 @@ def write_results(self, directory: Optional[Path] = None) -> None: write_results calls write_bands and write_dos if the DOS was calculated """ if directory is None: - directory = self.directory + directory = Path() self.write_bands(directory) @@ -246,7 +246,7 @@ def write_bands(self, directory=None) -> None: """ if directory is None: - directory = self.directory + directory = Path() kvec = [] for kpt in self.inputs.parameters.kpath.kpts: diff --git a/src/koopmans/references.bib b/src/koopmans/references.bib index aa1481785..1e8fe8ac2 100644 --- a/src/koopmans/references.bib +++ b/src/koopmans/references.bib @@ -1,26 +1,46 @@ -@article{Dabo2013, - title = {Donor and Acceptor Levels of Organic Photovoltaic Compounds from First Principles}, - 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 = {Phys. Chem. Chem. Phys.}, - volume = {15}, +@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 = {Rev. Mod. Phys.}, + volume = {73}, number = {2}, - pages = {685--695}, - issn = {14639076}, - doi = {10.1039/c2cp43491a}, - 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. {\copyright} the Owner Societies 2013.} + pages = {515--562}, + publisher = {American Physical Society}, + issn = {0034-6861}, + doi = {10.1103/RevModPhys.73.515}, + urldate = {2018-11-06} } -@misc{Dabo2009, - title = {Non-{{Koopmans Corrections}} in {{Density-functional Theory}}: {{Self-interaction Revisited}}}, - author = {Dabo, I. and Cococcioni, M. and Marzari, N.}, - year = {2009}, - month = jan, - eprint = {0901.2637}, - 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{Borghi2014, + title = {Koopmans-Compliant Functionals and Their Performance against Reference Molecular Data}, + author = {Borghi, Giovanni and Ferretti, Andrea and Nguyen, Ngoc Linh and Dabo, Ismaila and Marzari, Nicola}, + year = {2014}, + month = aug, + journal = {Phys. Rev. B}, + volume = {90}, + number = {7}, + pages = {075135}, + publisher = {American Physical Society}, + issn = {1098-0121}, + doi = {10.1103/PhysRevB.90.075135}, + urldate = {2017-11-23} } @article{Borghi2015, @@ -71,82 +91,30 @@ @article{Colonna2019 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{Nguyen2018, - title = {Koopmans-Compliant Spectral Functionals for Extended Systems}, - author = {Nguyen, Ngoc Linh and Colonna, Nicola and Ferretti, Andrea and Marzari, Nicola}, - year = {2018}, - month = may, - journal = {Phys. Rev. X}, - volume = {8}, - number = {2}, - pages = {021051}, - publisher = {American Physical Society}, - issn = {2160-3308}, - doi = {10.1103/PhysRevX.8.021051}, - urldate = {2019-03-23} -} - -@article{Nguyen2016, - title = {First-{{Principles Photoemission Spectroscopy}} of {{DNA}} and {{RNA Nucleobases}} from {{Koopmans-Compliant Functionals}}}, - author = {Nguyen, Ngoc Linh and Borghi, Giovanni and Ferretti, Andrea and Marzari, Nicola}, - year = {2016}, - month = aug, +@article{Colonna2022, + title = {Koopmans {{Spectral Functionals}} in {{Periodic Boundary Conditions}}}, + author = {Colonna, Nicola and De Gennaro, Riccardo and Linscott, Edward and Marzari, Nicola}, + year = {2022}, + month = sep, journal = {J. Chem. Theory Comput.}, - volume = {12}, - number = {8}, - pages = {3948--3958}, + volume = {18}, + number = {9}, + pages = {5435--5448}, publisher = {American Chemical Society}, - issn = {15499626}, - 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 {$<$}0.1 eV, but also that calculated photoemission spectra are in excellent agreement with experimental ultraviolet photoemission spectra. In particular, the role and contribution of different tautomers to the photoemission spectra are highlighted and discussed in detail. The structural properties of nucleobases are also investigated, showing an improved description with respect to local and semilocal density-functional theory. Methodologically, our results further consolidate the role of Koopmans-compliant functionals in providing, through orbital-density-dependent potentials, accurate electronic and spectral properties.} -} - -@article{Ferretti2014, - title = {Bridging Density-Functional and Many-Body Perturbation Theory: Orbital-Density Dependence in Electronic-Structure Functionals}, - author = {Ferretti, Andrea and Dabo, Ismaila and Cococcioni, Matteo and Marzari, Nicola}, - year = {2014}, - month = may, - journal = {Phys. Rev. B}, - volume = {89}, - number = {19}, - pages = {195134}, - publisher = {American Physical Society}, - issn = {1098-0121}, - doi = {10.1103/PhysRevB.89.195134}, - urldate = {2019-03-23} -} - -@article{Borghi2014, - title = {Koopmans-Compliant Functionals and Their Performance against Reference Molecular Data}, - author = {Borghi, Giovanni and Ferretti, Andrea and Nguyen, Ngoc Linh and Dabo, Ismaila and Marzari, Nicola}, - year = {2014}, - month = aug, - journal = {Phys. Rev. B}, - volume = {90}, - number = {7}, - pages = {075135}, - publisher = {American Physical Society}, - issn = {1098-0121}, - doi = {10.1103/PhysRevB.90.075135}, - urldate = {2017-11-23} + issn = {1549-9618}, + doi = {10.1021/acs.jctc.2c00161}, + urldate = {2024-03-05}, + 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.} } -@article{Pederson1984, - title = {Local-density {{Hartree}}--{{Fock}} Theory of Electronic States of Molecules with Self-interaction Correction}, - author = {Pederson, Mark R. and Heaton, Richard A. and Lin, Chun C.}, - year = {1984}, - month = mar, - journal = {J. Chem. Phys.}, - volume = {80}, - number = {5}, - pages = {1972--1975}, - publisher = {American Institute of Physics}, - issn = {0021-9606}, - doi = {10.1063/1.446959}, - urldate = {2019-03-23}, - abstract = {A scheme for incorporating the self-interaction correction (SIC) to the local density approximation of the Hartree--Fock theory of electronic structure of molecules is presented. This method is applied to the N2 molecule and the resulting orbital energies and total energy are in good agreement with the Hartree--Fock values.}, - keywords = {ELECTRONIC STRUCTURE,HARTREEFOCK METHOD,MOLECULES,NITROGEN} +@misc{Dabo2009, + title = {Non-{{Koopmans Corrections}} in {{Density-functional Theory}}: {{Self-interaction Revisited}}}, + author = {Dabo, I. and Cococcioni, M. and Marzari, N.}, + year = {2009}, + month = jan, + eprint = {0901.2637}, + 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, @@ -164,34 +132,51 @@ @article{Dabo2010 urldate = {2017-11-23} } -@article{Nattino2019, - title = {Functional {{Extrapolations}} to {{Tame Unbound Anions}} in {{Density-Functional Theory Calculations}}}, - author = {Nattino, Francesco and Dupont, C{\'e}line and Marzari, Nicola and Andreussi, Oliviero}, - year = {2019}, - month = nov, - journal = {J. Chem. Theory Comput.}, +@article{Dabo2013, + title = {Donor and Acceptor Levels of Organic Photovoltaic Compounds from First Principles}, + 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 = {Phys. Chem. Chem. Phys.}, volume = {15}, - number = {11}, - pages = {6313--6322}, - issn = {15499626}, - doi = {10.1021/acs.jctc.9b00552}, - 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.} + number = {2}, + pages = {685--695}, + issn = {14639076}, + doi = {10.1039/c2cp43491a}, + 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. {\copyright} the Owner Societies 2013.} } -@article{Marzari2012, - title = {Maximally Localized {{Wannier}} Functions: {{Theory}} and Applications}, - author = {Marzari, Nicola and Mostofi, Arash A. and Yates, Jonathan R. and Souza, Ivo and Vanderbilt, David}, - year = {2012}, - month = oct, - journal = {Rev. Mod. Phys.}, - volume = {84}, - number = {4}, - pages = {1419--1475}, +@article{DeGennaro2022, + title = {Bloch's Theorem in Orbital-Density-Dependent Functionals: {{Band}} Structures from {{Koopmans}} Spectral Functionals}, + shorttitle = {Bloch's Theorem in Orbital-Density-Dependent Functionals}, + author = {De Gennaro, Riccardo and Colonna, Nicola and Linscott, Edward and Marzari, Nicola}, + year = {2022}, + month = jul, + journal = {Phys. Rev. B}, + volume = {106}, + number = {3}, + pages = {035106}, publisher = {American Physical Society}, - issn = {0034-6861}, - doi = {10.1103/RevModPhys.84.1419}, - urldate = {2018-08-29} + 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} +} + +@article{Ferretti2014, + title = {Bridging Density-Functional and Many-Body Perturbation Theory: Orbital-Density Dependence in Electronic-Structure Functionals}, + author = {Ferretti, Andrea and Dabo, Ismaila and Cococcioni, Matteo and Marzari, Nicola}, + year = {2014}, + month = may, + journal = {Phys. Rev. B}, + volume = {89}, + number = {19}, + pages = {195134}, + publisher = {American Physical Society}, + issn = {1098-0121}, + doi = {10.1103/PhysRevB.89.195134}, + urldate = {2019-03-23} } @article{Hamann2013, @@ -210,55 +195,36 @@ @article{Hamann2013 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. {\copyright} 2013 American Physical Society.} } -@article{Schlipf2015, - title = {Optimization Algorithm for the Generation of {{ONCV}} Pseudopotentials}, - author = {Schlipf, Martin and Gygi, Fran{\c c}ois}, - year = {2015}, - month = nov, - journal = {Computer Physics Communications}, - volume = {196}, - pages = {36--44}, - issn = {0010-4655}, - doi = {10.1016/j.cpc.2015.05.011}, - urldate = {2021-07-09}, - abstract = {We present an optimization algorithm to construct pseudopotentials and use it to generate a set of Optimized Norm-Conserving Vanderbilt (ONCV) pseudopotentials for elements up to Z=83 (Bi) (excluding Lanthanides). We introduce a quality function that assesses the agreement of a pseudopotential calculation with all-electron FLAPW results, and the necessary plane-wave energy cutoff. This quality function allows us to use a Nelder--Mead optimization algorithm on a training set of materials to optimize the input parameters of the pseudopotential construction for most of the periodic table. We control the accuracy of the resulting pseudopotentials on a test set of materials independent of the training set. We find that the automatically constructed pseudopotentials (http://www.quantum-simulation.org) provide a good agreement with the all-electron results obtained using the FLEUR code with a plane-wave energy cutoff of approximately 60 Ry.}, - keywords = {All-electron calculation,Condensed matter,Density functional theory,Plane wave,Pseudopotential} +@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{Scherpelz2016, - title = {Implementation and {{Validation}} of {{Fully Relativistic GW Calculations}}: {{Spin}}--{{Orbit Coupling}} in {{Molecules}}, {{Nanocrystals}}, and {{Solids}}}, - shorttitle = {Implementation and {{Validation}} of {{Fully Relativistic GW Calculations}}}, - author = {Scherpelz, Peter and Govoni, Marco and Hamada, Ikutaro and Galli, Giulia}, - year = {2016}, - month = aug, +@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 = {12}, - number = {8}, - pages = {3523--3544}, + volume = {8}, + number = {5}, + pages = {1515--1531}, publisher = {American Chemical Society}, issn = {1549-9618}, - doi = {10.1021/acs.jctc.6b00114}, - urldate = {2022-02-17}, - abstract = {We present an implementation of G0W0 calculations including spin--orbit coupling (SOC) enabling investigations of large systems, with thousands of electrons, and we discuss results for molecules, solids, and nanocrystals. Using a newly developed set of molecules with heavy elements (called GW-SOC81), we find that, when based upon hybrid density functional calculations, fully relativistic (FR) and scalar-relativistic (SR) G0W0 calculations of vertical ionization potentials both yield excellent performance compared to experiment, with errors below 1.9\%. We demonstrate that while SR calculations have higher random errors, FR calculations systematically underestimate the VIP by 0.1 to 0.2 eV. We further verify that SOC effects may be well approximated at the FR density functional level and then added to SR G0W0 results for a broad class of systems. We also address the use of different root-finding algorithms for the G0W0 quasiparticle equation and the significant influence of including d electrons in the valence partition of the pseudopotential for G0W0 calculations. Finally, we present statistical analyses of our data, highlighting the importance of separating definitive improvements from those that may occur by chance due to a limited number of samples. We suggest the statistical analyses used here will be useful in the assessment of the accuracy of a large variety of electronic structure methods.} -} - -@article{Prandini2018, - title = {Precision and Efficiency in Solid-State Pseudopotential Calculations}, - author = {Prandini, Gianluca and Marrazzo, Antimo and Castelli, Ivano E. and Mounet, Nicolas and Marzari, Nicola}, - year = {2018}, - month = dec, - journal = {npj Comput Mater}, - volume = {4}, - number = {1}, - pages = {1--13}, - publisher = {Nature Publishing Group}, - issn = {2057-3960}, - doi = {10.1038/s41524-018-0127-2}, - urldate = {2022-02-17}, - abstract = {Despite the enormous success and popularity of density-functional theory, systematic verification and validation studies are still limited in number and scope. Here, we propose a protocol to test publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain curated pseudopotential libraries (named SSSP or standard solid-state pseudopotential libraries), that we target for high-throughput materials screening (``SSSP efficiency'') and high-precision materials modelling (``SSSP precision''). This latter scores highest among open-source pseudopotential libraries available in the {$\Delta$}-factor test of equations of states of elemental solids.}, - copyright = {2018 The Author(s)}, - langid = {english}, - keywords = {Computational methods,Electronic structure} + 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--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--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, @@ -275,68 +241,32 @@ @article{Lejaeghere2016 urldate = {2022-02-17} } -@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 = {Rev. Mod. Phys.}, - volume = {73}, - number = {2}, - pages = {515--562}, - publisher = {American Physical Society}, - issn = {0034-6861}, - doi = {10.1103/RevModPhys.73.515}, - urldate = {2018-11-06} -} - -@article{DeGennaro2022, - title = {Bloch's Theorem in Orbital-Density-Dependent Functionals: {{Band}} Structures from {{Koopmans}} Spectral Functionals}, - shorttitle = {Bloch's Theorem in Orbital-Density-Dependent Functionals}, - author = {De Gennaro, Riccardo and Colonna, Nicola and Linscott, Edward and Marzari, Nicola}, - year = {2022}, - month = jul, - journal = {Phys. Rev. B}, - volume = {106}, - number = {3}, - 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} -} - -@article{vanSetten2018, - title = {The {{PseudoDojo}}: {{Training}} and Grading a 85 Element Optimized Norm-Conserving Pseudopotential Table}, - shorttitle = {The {{PseudoDojo}}}, - author = {{van Setten}, M. J. and Giantomassi, M. and Bousquet, E. and Verstraete, M. J. and Hamann, D. R. and Gonze, X. and Rignanese, G. -M.}, +@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}, - month = may, - journal = {Computer Physics Communications}, - volume = {226}, - pages = {39--54}, - issn = {0010-4655}, - doi = {10.1016/j.cpc.2018.01.012}, - urldate = {2022-07-29}, - abstract = {First-principles calculations in crystalline structures are often performed with a planewave basis set. To make the number of basis functions tractable two approximations are usually introduced: core electrons are frozen and the diverging Coulomb potential near the nucleus is replaced by a smoother expression. The norm-conserving pseudopotential was the first successful method to apply these approximations in a fully ab initio way. Later on, more efficient and more exact approaches were developed based on the ultrasoft and the projector augmented wave formalisms. These formalisms are however more complex and developing new features in these frameworks is usually more difficult than in the norm-conserving framework. Most of the existing tables of norm-conserving pseudopotentials, generated long ago, do not include the latest developments, are not systematically tested or are not designed primarily for high precision. In this paper, we present our PseudoDojo framework for developing and testing full tables of pseudopotentials, and demonstrate it with a new table generated with the ONCVPSP approach. The PseudoDojo is an open source project, building on the AbiPy package, for developing and systematically testing pseudopotentials. At present it contains 7 different batteries of tests executed with ABINIT, which are performed as a function of the energy cutoff. The results of these tests are then used to provide hints for the energy cutoff for actual production calculations. Our final set contains 141 pseudopotentials split into a standard and a stringent accuracy table. In total around 70,000 calculations were performed to test the pseudopotentials. The process of developing the final table led to new insights into the effects of both the core-valence partitioning and the non-linear core corrections on the stability, convergence, and transferability of norm-conserving pseudopotentials. The PseudoDojo hence provides a set of pseudopotentials and general purpose tools for further testing and development, focusing on highly accurate calculations and their use in the development of ab initio packages. The pseudopotential files are available on the PseudoDojo web-interface pseudo-dojo.org under the name NC (ONCVPSP) v0.4 in the psp8, UPF2, and PSML 1.1 formats. The webinterface also provides the inputs, which are compatible with the 3.3.1 and higher versions of ONCVPSP. All tests have been performed with ABINIT 8.4.}, - langid = {english}, - keywords = {Density functional theory,Electronic structure,First-principles calculation,Pseudopotential} + journal = {Natl. Sci. Rev.}, + volume = {5}, + pages = {203--215}, + url = {https://academic.oup.com/nsr/article/5/2/203/4104965}, + urldate = {2020-04-04} } -@article{Schubert2023, - title = {Testing {{Koopmans}} Spectral Functionals on the Analytically Solvable {{Hooke}}'s Atom}, - author = {Schubert, Yannick and Marzari, Nicola and Linscott, Edward}, +@article{Linscott2023, + title = {Koopmans: {{An Open-Source Package}} for {{Accurately}} and {{Efficiently Predicting Spectral Properties}} with {{Koopmans Functionals}}}, + shorttitle = {Koopmans}, + author = {Linscott, Edward B. 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 = apr, - journal = {The Journal of Chemical Physics}, - volume = {158}, - number = {14}, - pages = {144113}, - issn = {0021-9606}, - doi = {10.1063/5.0138610}, - urldate = {2023-04-20}, - abstract = {Koopmans spectral functionals are a class of orbital-density-dependent functionals designed to accurately predict spectroscopic properties. They do so markedly better than their Kohn--Sham density-functional theory counterparts, as demonstrated in earlier works on benchmarks of molecules and bulk systems. This work is a complementary study where---instead of comparing against real, many-electron systems---we test Koopmans spectral functionals on Hooke's atom, a toy two-electron system that has analytical solutions for particular strengths of its harmonic confining potential. As these calculations clearly illustrate, Koopmans spectral functionals do an excellent job of describing Hooke's atom across a range of confining potential strengths. This work also provides broader insights into the features and capabilities of Koopmans spectral functionals more generally.} + month = oct, + journal = {J. Chem. Theory Comput.}, + volume = {19}, + number = {20}, + pages = {7097--7111}, + publisher = {American Chemical Society}, + issn = {1549-9618}, + doi = {10.1021/acs.jctc.3c00652}, + urldate = {2024-03-05}, + abstract = {Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional framework. These functionals impose a generalized piecewise linearity condition to the entire electronic manifold, ensuring that orbital energies match the corresponding electron removal/addition energy differences (in contrast to semilocal DFT, where a mismatch between the two lies at the heart of the band gap problem and, more generally, the unreliability of Kohn--Sham orbital energies). This strategy has proven to be very powerful, yielding molecular orbital energies and solid-state band structures with comparable accuracy to many-body perturbation theory but at greatly reduced computational cost while preserving a functional formulation. This paper reviews the theory of Koopmans functionals, discusses the algorithms necessary for their implementation, and introduces koopmans, an open-source package that contains all of the code and workflows needed to perform Koopmans functional calculations and obtain reliable spectral properties of molecules and materials.} } @article{Ma2016, @@ -357,92 +287,34 @@ @article{Ma2016 langid = {english} } -@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{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} -} - -@article{Skone2016, - title = {Nonempirical Range-Separated Hybrid Functionals for Solids and Molecules}, - author = {Skone, Jonathan H. and Govoni, Marco and Galli, Giulia}, - year = {2016}, - month = jun, - journal = {Phys. Rev. B}, - volume = {93}, - number = {23}, - pages = {235106}, +@article{Marzari2012, + title = {Maximally Localized {{Wannier}} Functions: {{Theory}} and Applications}, + author = {Marzari, Nicola and Mostofi, Arash A. and Yates, Jonathan R. and Souza, Ivo and Vanderbilt, David}, + year = {2012}, + month = oct, + journal = {Rev. Mod. Phys.}, + volume = {84}, + number = {4}, + pages = {1419--1475}, publisher = {American Physical Society}, - issn = {24699969}, - doi = {10.1103/PhysRevB.93.235106}, - urldate = {2020-05-10}, - abstract = {Dielectric-dependent hybrid (DDH) functionals were recently shown to yield accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than that of GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. Here we introduce a range-separated (RS) version of DDH functionals where short- and long-range components are matched using system-dependent, nonempirical parameters. We show that RS-DDHs yield accurate electronic properties of inorganic and organic solids, including energy gaps and absolute ionization potentials. Furthermore we show that these functionals may be generalized to finite systems.} -} - -@article{Wing2021, - title = {Band Gaps of Crystalline Solids from {{Wannier-localization}}--Based Optimal Tuning of a Screened Range-Separated Hybrid Functional}, - author = {Wing, Dahvyd and Ohad, Guy and Haber, Jonah B. and Filip, Marina R. and Gant, Stephen E. and Neaton, Jeffrey B. and Kronik, Leeor}, - year = {2021}, - month = aug, - journal = {Proc. Natl. Acad. Sci.}, - volume = {118}, - number = {34}, - pages = {e2104556118}, - publisher = {Proceedings of the National Academy of Sciences}, - doi = {10.1073/pnas.2104556118}, - urldate = {2022-03-22} + issn = {0034-6861}, + doi = {10.1103/RevModPhys.84.1419}, + urldate = {2018-08-29} } -@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, +@article{Nattino2019, + title = {Functional {{Extrapolations}} to {{Tame Unbound Anions}} in {{Density-Functional Theory Calculations}}}, + author = {Nattino, Francesco and Dupont, C{\'e}line and Marzari, Nicola and Andreussi, Oliviero}, + year = {2019}, + month = nov, 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--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--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{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.} + volume = {15}, + number = {11}, + pages = {6313--6322}, + issn = {15499626}, + doi = {10.1021/acs.jctc.9b00552}, + 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, @@ -460,21 +332,71 @@ @article{Nguyen2015 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---i.e., with respect to charged excitations---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{Qiao2023a, - title = {Automated Mixing of Maximally Localized {{Wannier}} Functions into Target Manifolds}, - author = {Qiao, Junfeng and Pizzi, Giovanni and Marzari, Nicola}, - year = {2023}, - month = oct, +@article{Nguyen2016, + title = {First-{{Principles Photoemission Spectroscopy}} of {{DNA}} and {{RNA Nucleobases}} from {{Koopmans-Compliant Functionals}}}, + author = {Nguyen, Ngoc Linh and Borghi, Giovanni and Ferretti, Andrea and Marzari, Nicola}, + year = {2016}, + month = aug, + journal = {J. Chem. Theory Comput.}, + volume = {12}, + number = {8}, + pages = {3948--3958}, + publisher = {American Chemical Society}, + issn = {15499626}, + 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 {$<$}0.1 eV, but also that calculated photoemission spectra are in excellent agreement with experimental ultraviolet photoemission spectra. In particular, the role and contribution of different tautomers to the photoemission spectra are highlighted and discussed in detail. The structural properties of nucleobases are also investigated, showing an improved description with respect to local and semilocal density-functional theory. Methodologically, our results further consolidate the role of Koopmans-compliant functionals in providing, through orbital-density-dependent potentials, accurate electronic and spectral properties.} +} + +@article{Nguyen2018, + title = {Koopmans-Compliant Spectral Functionals for Extended Systems}, + author = {Nguyen, Ngoc Linh and Colonna, Nicola and Ferretti, Andrea and Marzari, Nicola}, + year = {2018}, + month = may, + journal = {Phys. Rev. X}, + volume = {8}, + number = {2}, + pages = {021051}, + publisher = {American Physical Society}, + issn = {2160-3308}, + doi = {10.1103/PhysRevX.8.021051}, + urldate = {2019-03-23} +} + +@article{Pederson1984, + title = {Local-density {{Hartree}}--{{Fock}} Theory of Electronic States of Molecules with Self-interaction Correction}, + author = {Pederson, Mark R. and Heaton, Richard A. and Lin, Chun C.}, + year = {1984}, + month = mar, + journal = {J. Chem. Phys.}, + volume = {80}, + number = {5}, + pages = {1972--1975}, + publisher = {American Institute of Physics}, + issn = {0021-9606}, + doi = {10.1063/1.446959}, + urldate = {2019-03-23}, + abstract = {A scheme for incorporating the self-interaction correction (SIC) to the local density approximation of the Hartree--Fock theory of electronic structure of molecules is presented. This method is applied to the N2 molecule and the resulting orbital energies and total energy are in good agreement with the Hartree--Fock values.}, + keywords = {ELECTRONIC STRUCTURE,HARTREEFOCK METHOD,MOLECULES,NITROGEN} +} + +@article{Prandini2018, + title = {Precision and Efficiency in Solid-State Pseudopotential Calculations}, + author = {Prandini, Gianluca and Marrazzo, Antimo and Castelli, Ivano E. and Mounet, Nicolas and Marzari, Nicola}, + year = {2018}, + month = dec, journal = {npj Comput Mater}, - volume = {9}, - pages = {206}, + volume = {4}, + number = {1}, + pages = {1--13}, + publisher = {Nature Publishing Group}, issn = {2057-3960}, - doi = {10.1038/s41524-023-01147-9}, - urldate = {2023-11-23}, - abstract = {Maximally localized Wannier functions (MLWFs) are widely used in electronic-structure calculations. We have recently developed automated approaches to generate MLWFs that represent natural tight-binding sets of atomic-like orbitals; these describe accurately both the occupied states and the complementary unoccupied ones. For many applications, it is required to use MLWFs that describe instead certain target groups of bands: the valence or the conduction bands, or correlated manifolds. Here, we start from these tight-binding sets of MLWFs, and mix them using a combination of parallel transport and maximal localization to construct manifold-remixed Wannier functions (MRWFs): these are orthogonal sets of MLWFs that fully and only span desired target submanifolds. The algorithm is simple and robust, and is showcased here in reference applications (silicon, MoS2, and SrVO3) and in a mid-throughput study of 77 insulators.}, - copyright = {2023 The Author(s)}, + doi = {10.1038/s41524-018-0127-2}, + urldate = {2022-02-17}, + abstract = {Despite the enormous success and popularity of density-functional theory, systematic verification and validation studies are still limited in number and scope. Here, we propose a protocol to test publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain curated pseudopotential libraries (named SSSP or standard solid-state pseudopotential libraries), that we target for high-throughput materials screening (``SSSP efficiency'') and high-precision materials modelling (``SSSP precision''). This latter scores highest among open-source pseudopotential libraries available in the {$\Delta$}-factor test of equations of states of elemental solids.}, + copyright = {2018 The Author(s)}, langid = {english}, - keywords = {Electronic properties and materials,Electronic structure} + keywords = {Computational methods,Electronic structure} } @article{Qiao2023, @@ -494,21 +416,115 @@ @article{Qiao2023 keywords = {Computational methods,Electronic structure} } -@article{Linscott2023, - title = {Koopmans: {{An Open-Source Package}} for {{Accurately}} and {{Efficiently Predicting Spectral Properties}} with {{Koopmans Functionals}}}, - shorttitle = {Koopmans}, - author = {Linscott, Edward B. and Colonna, Nicola and De Gennaro, Riccardo and Nguyen, Ngoc Linh and Borghi, Giovanni and Ferretti, Andrea and Dabo, Ismaila and Marzari, Nicola}, +@article{Qiao2023a, + title = {Automated Mixing of Maximally Localized {{Wannier}} Functions into Target Manifolds}, + author = {Qiao, Junfeng and Pizzi, Giovanni and Marzari, Nicola}, year = {2023}, month = oct, + journal = {npj Comput Mater}, + volume = {9}, + pages = {206}, + issn = {2057-3960}, + doi = {10.1038/s41524-023-01147-9}, + urldate = {2023-11-23}, + abstract = {Maximally localized Wannier functions (MLWFs) are widely used in electronic-structure calculations. We have recently developed automated approaches to generate MLWFs that represent natural tight-binding sets of atomic-like orbitals; these describe accurately both the occupied states and the complementary unoccupied ones. For many applications, it is required to use MLWFs that describe instead certain target groups of bands: the valence or the conduction bands, or correlated manifolds. Here, we start from these tight-binding sets of MLWFs, and mix them using a combination of parallel transport and maximal localization to construct manifold-remixed Wannier functions (MRWFs): these are orthogonal sets of MLWFs that fully and only span desired target submanifolds. The algorithm is simple and robust, and is showcased here in reference applications (silicon, MoS2, and SrVO3) and in a mid-throughput study of 77 insulators.}, + copyright = {2023 The Author(s)}, + langid = {english}, + keywords = {Electronic properties and materials,Electronic structure} +} + +@article{Scherpelz2016, + title = {Implementation and {{Validation}} of {{Fully Relativistic GW Calculations}}: {{Spin}}--{{Orbit Coupling}} in {{Molecules}}, {{Nanocrystals}}, and {{Solids}}}, + shorttitle = {Implementation and {{Validation}} of {{Fully Relativistic GW Calculations}}}, + author = {Scherpelz, Peter and Govoni, Marco and Hamada, Ikutaro and Galli, Giulia}, + year = {2016}, + month = aug, journal = {J. Chem. Theory Comput.}, - volume = {19}, - number = {20}, - pages = {7097--7111}, + volume = {12}, + number = {8}, + pages = {3523--3544}, publisher = {American Chemical Society}, issn = {1549-9618}, - doi = {10.1021/acs.jctc.3c00652}, - urldate = {2024-03-05}, - abstract = {Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional framework. These functionals impose a generalized piecewise linearity condition to the entire electronic manifold, ensuring that orbital energies match the corresponding electron removal/addition energy differences (in contrast to semilocal DFT, where a mismatch between the two lies at the heart of the band gap problem and, more generally, the unreliability of Kohn--Sham orbital energies). This strategy has proven to be very powerful, yielding molecular orbital energies and solid-state band structures with comparable accuracy to many-body perturbation theory but at greatly reduced computational cost while preserving a functional formulation. This paper reviews the theory of Koopmans functionals, discusses the algorithms necessary for their implementation, and introduces koopmans, an open-source package that contains all of the code and workflows needed to perform Koopmans functional calculations and obtain reliable spectral properties of molecules and materials.} + doi = {10.1021/acs.jctc.6b00114}, + urldate = {2022-02-17}, + abstract = {We present an implementation of G0W0 calculations including spin--orbit coupling (SOC) enabling investigations of large systems, with thousands of electrons, and we discuss results for molecules, solids, and nanocrystals. Using a newly developed set of molecules with heavy elements (called GW-SOC81), we find that, when based upon hybrid density functional calculations, fully relativistic (FR) and scalar-relativistic (SR) G0W0 calculations of vertical ionization potentials both yield excellent performance compared to experiment, with errors below 1.9\%. We demonstrate that while SR calculations have higher random errors, FR calculations systematically underestimate the VIP by 0.1 to 0.2 eV. We further verify that SOC effects may be well approximated at the FR density functional level and then added to SR G0W0 results for a broad class of systems. We also address the use of different root-finding algorithms for the G0W0 quasiparticle equation and the significant influence of including d electrons in the valence partition of the pseudopotential for G0W0 calculations. Finally, we present statistical analyses of our data, highlighting the importance of separating definitive improvements from those that may occur by chance due to a limited number of samples. We suggest the statistical analyses used here will be useful in the assessment of the accuracy of a large variety of electronic structure methods.} +} + +@article{Schlipf2015, + title = {Optimization Algorithm for the Generation of {{ONCV}} Pseudopotentials}, + author = {Schlipf, Martin and Gygi, Fran{\c c}ois}, + year = {2015}, + month = nov, + journal = {Computer Physics Communications}, + volume = {196}, + pages = {36--44}, + issn = {0010-4655}, + doi = {10.1016/j.cpc.2015.05.011}, + urldate = {2021-07-09}, + abstract = {We present an optimization algorithm to construct pseudopotentials and use it to generate a set of Optimized Norm-Conserving Vanderbilt (ONCV) pseudopotentials for elements up to Z=83 (Bi) (excluding Lanthanides). We introduce a quality function that assesses the agreement of a pseudopotential calculation with all-electron FLAPW results, and the necessary plane-wave energy cutoff. This quality function allows us to use a Nelder--Mead optimization algorithm on a training set of materials to optimize the input parameters of the pseudopotential construction for most of the periodic table. We control the accuracy of the resulting pseudopotentials on a test set of materials independent of the training set. We find that the automatically constructed pseudopotentials (http://www.quantum-simulation.org) provide a good agreement with the all-electron results obtained using the FLEUR code with a plane-wave energy cutoff of approximately 60 Ry.}, + keywords = {All-electron calculation,Condensed matter,Density functional theory,Plane wave,Pseudopotential} +} + +@article{Schubert2023, + title = {Testing {{Koopmans}} Spectral Functionals on the Analytically Solvable {{Hooke}}'s Atom}, + author = {Schubert, Yannick and Marzari, Nicola and Linscott, Edward}, + year = {2023}, + month = apr, + journal = {The Journal of Chemical Physics}, + volume = {158}, + number = {14}, + pages = {144113}, + issn = {0021-9606}, + doi = {10.1063/5.0138610}, + urldate = {2023-04-20}, + abstract = {Koopmans spectral functionals are a class of orbital-density-dependent functionals designed to accurately predict spectroscopic properties. They do so markedly better than their Kohn--Sham density-functional theory counterparts, as demonstrated in earlier works on benchmarks of molecules and bulk systems. This work is a complementary study where---instead of comparing against real, many-electron systems---we test Koopmans spectral functionals on Hooke's atom, a toy two-electron system that has analytical solutions for particular strengths of its harmonic confining potential. As these calculations clearly illustrate, Koopmans spectral functionals do an excellent job of describing Hooke's atom across a range of confining potential strengths. This work also provides broader insights into the features and capabilities of Koopmans spectral functionals more generally.} +} + +@article{Skone2016, + title = {Nonempirical Range-Separated Hybrid Functionals for Solids and Molecules}, + author = {Skone, Jonathan H. and Govoni, Marco and Galli, Giulia}, + year = {2016}, + month = jun, + journal = {Phys. Rev. B}, + volume = {93}, + number = {23}, + pages = {235106}, + publisher = {American Physical Society}, + issn = {24699969}, + doi = {10.1103/PhysRevB.93.235106}, + urldate = {2020-05-10}, + abstract = {Dielectric-dependent hybrid (DDH) functionals were recently shown to yield accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than that of GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. Here we introduce a range-separated (RS) version of DDH functionals where short- and long-range components are matched using system-dependent, nonempirical parameters. We show that RS-DDHs yield accurate electronic properties of inorganic and organic solids, including energy gaps and absolute ionization potentials. Furthermore we show that these functionals may be generalized to finite systems.} +} + +@article{vanSetten2018, + title = {The {{PseudoDojo}}: {{Training}} and Grading a 85 Element Optimized Norm-Conserving Pseudopotential Table}, + shorttitle = {The {{PseudoDojo}}}, + author = {{van Setten}, M. J. and Giantomassi, M. and Bousquet, E. and Verstraete, M. J. and Hamann, D. R. and Gonze, X. and Rignanese, G. -M.}, + year = {2018}, + month = may, + journal = {Computer Physics Communications}, + volume = {226}, + pages = {39--54}, + issn = {0010-4655}, + doi = {10.1016/j.cpc.2018.01.012}, + urldate = {2022-07-29}, + abstract = {First-principles calculations in crystalline structures are often performed with a planewave basis set. To make the number of basis functions tractable two approximations are usually introduced: core electrons are frozen and the diverging Coulomb potential near the nucleus is replaced by a smoother expression. The norm-conserving pseudopotential was the first successful method to apply these approximations in a fully ab initio way. Later on, more efficient and more exact approaches were developed based on the ultrasoft and the projector augmented wave formalisms. These formalisms are however more complex and developing new features in these frameworks is usually more difficult than in the norm-conserving framework. Most of the existing tables of norm-conserving pseudopotentials, generated long ago, do not include the latest developments, are not systematically tested or are not designed primarily for high precision. In this paper, we present our PseudoDojo framework for developing and testing full tables of pseudopotentials, and demonstrate it with a new table generated with the ONCVPSP approach. The PseudoDojo is an open source project, building on the AbiPy package, for developing and systematically testing pseudopotentials. At present it contains 7 different batteries of tests executed with ABINIT, which are performed as a function of the energy cutoff. The results of these tests are then used to provide hints for the energy cutoff for actual production calculations. Our final set contains 141 pseudopotentials split into a standard and a stringent accuracy table. In total around 70,000 calculations were performed to test the pseudopotentials. The process of developing the final table led to new insights into the effects of both the core-valence partitioning and the non-linear core corrections on the stability, convergence, and transferability of norm-conserving pseudopotentials. The PseudoDojo hence provides a set of pseudopotentials and general purpose tools for further testing and development, focusing on highly accurate calculations and their use in the development of ab initio packages. The pseudopotential files are available on the PseudoDojo web-interface pseudo-dojo.org under the name NC (ONCVPSP) v0.4 in the psp8, UPF2, and PSML 1.1 formats. The webinterface also provides the inputs, which are compatible with the 3.3.1 and higher versions of ONCVPSP. All tests have been performed with ABINIT 8.4.}, + langid = {english}, + keywords = {Density functional theory,Electronic structure,First-principles calculation,Pseudopotential} +} + +@article{Wing2021, + title = {Band Gaps of Crystalline Solids from {{Wannier-localization}}--Based Optimal Tuning of a Screened Range-Separated Hybrid Functional}, + author = {Wing, Dahvyd and Ohad, Guy and Haber, Jonah B. and Filip, Marina R. and Gant, Stephen E. and Neaton, Jeffrey B. and Kronik, Leeor}, + year = {2021}, + month = aug, + journal = {Proc. Natl. Acad. Sci.}, + volume = {118}, + number = {34}, + pages = {e2104556118}, + publisher = {Proceedings of the National Academy of Sciences}, + doi = {10.1073/pnas.2104556118}, + urldate = {2022-03-22} } @misc{zotero-3342, @@ -516,19 +532,3 @@ @misc{zotero-3342 url = {https://pubs.acs.org/doi/full/10.1021/acs.jctc.2c00161}, urldate = {2024-03-05} } - -@article{Colonna2022, - title = {Koopmans {{Spectral Functionals}} in {{Periodic Boundary Conditions}}}, - author = {Colonna, Nicola and De Gennaro, Riccardo and Linscott, Edward and Marzari, Nicola}, - year = {2022}, - month = sep, - journal = {J. Chem. Theory Comput.}, - volume = {18}, - number = {9}, - pages = {5435--5448}, - publisher = {American Chemical Society}, - issn = {1549-9618}, - doi = {10.1021/acs.jctc.2c00161}, - urldate = {2024-03-05}, - 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.} -} diff --git a/src/koopmans/utils/__init__.py b/src/koopmans/utils/__init__.py index 0afdd764f..ab84f6690 100644 --- a/src/koopmans/utils/__init__.py +++ b/src/koopmans/utils/__init__.py @@ -19,7 +19,7 @@ read_atomic_positions, read_cell_parameters, read_wannier_hr_file, write_alpha_file) from ._misc import flatten, update_nested_dict -from ._os import (HasDirectoryAttr, chdir, copy, find_executable, +from ._os import (HasDirectoryInfo, chdir, copy, find_executable, get_binary_content, get_content, remove, set_env, symlink, symlink_tree, system_call, write_binary_content, write_content) diff --git a/src/koopmans/utils/_io.py b/src/koopmans/utils/_io.py index fbd829a2e..300a27879 100644 --- a/src/koopmans/utils/_io.py +++ b/src/koopmans/utils/_io.py @@ -23,7 +23,7 @@ from koopmans.cell import (cell_follows_qe_conventions, cell_to_parameters, parameters_to_cell) -from ._os import HasDirectoryAttr, get_content +from ._os import HasDirectoryInfo, get_content def parse_dict(dct: Dict[str, Any]) -> Dict[str, Any]: @@ -293,7 +293,7 @@ def parse_wannier_hr_file_contents(lines: List[str]) -> Tuple[np.ndarray, np.nda return hr_np, rvect_np, weights, nrpts -def read_wannier_hr_file(src_calc_path: Tuple[HasDirectoryAttr, Path]) -> Tuple[np.ndarray, np.ndarray, List[int], int]: +def read_wannier_hr_file(src_calc_path: Tuple[HasDirectoryInfo, Path]) -> Tuple[np.ndarray, np.ndarray, List[int], int]: lines = get_content(*src_calc_path) return parse_wannier_hr_file_contents(lines) diff --git a/src/koopmans/utils/_os.py b/src/koopmans/utils/_os.py index 1911d42dd..e3782f8a8 100644 --- a/src/koopmans/utils/_os.py +++ b/src/koopmans/utils/_os.py @@ -186,15 +186,19 @@ def is_exe(fpath: Path): @runtime_checkable -class HasDirectoryAttr(Protocol): +class HasDirectoryInfo(Protocol): directory: Path | None + @property + def absolute_directory(self) -> Path | None: + ... -def get_binary_content(source: HasDirectoryAttr, relpath: Path | str) -> bytes: + +def get_binary_content(source: HasDirectoryInfo, relpath: Path | str) -> bytes: if isinstance(relpath, str): relpath = Path(relpath) - assert source.directory is not None - with open(source.directory / relpath, "rb") as f: + assert source.absolute_directory is not None + with open(source.absolute_directory / relpath, "rb") as f: flines = f.read() return flines @@ -207,14 +211,14 @@ def write_binary_content(dst_file: Path | str, merged_filecontents: bytes): f.write(merged_filecontents) -def get_content(source: HasDirectoryAttr | None, relpath: Path | str) -> List[str]: +def get_content(source: HasDirectoryInfo | None, relpath: Path | str) -> List[str]: if isinstance(relpath, str): relpath = Path(relpath) - if source is None or source.directory is None: + if source is None or source.absolute_directory is None: full_path = relpath else: - full_path = source.directory / relpath + full_path = source.absolute_directory / relpath with open(full_path, "r") as f: flines = [l.strip('\n') for l in f.readlines()] diff --git a/src/koopmans/workflows/_convergence.py b/src/koopmans/workflows/_convergence.py index 7335166e8..28afa3b56 100644 --- a/src/koopmans/workflows/_convergence.py +++ b/src/koopmans/workflows/_convergence.py @@ -452,9 +452,8 @@ def ConvergenceWorkflowFactory(subworkflow: Workflow, observable: Union[str, Cal observable = ObservableFactory(observable) if isinstance( observable, str) else observable - # Co-opt the fromparent method to use the subworkflow settings to initialize a ConvergenceWorkflow... - wf = ConvergenceWorkflow.fromparent(subworkflow, subworkflow_class=subworkflow.__class__, + # Initialize a ConvergenceWorkflow copying the settings of the subworkflow + wf = ConvergenceWorkflow.from_other(subworkflow, subworkflow_class=subworkflow.__class__, variables=variables, observable=observable, threshold=threshold) - wf.parent = None # ... making sure we remove wf.parent immediately afterwards return wf diff --git a/src/koopmans/workflows/_dft.py b/src/koopmans/workflows/_dft.py index 154e4a123..ffeec47e9 100644 --- a/src/koopmans/workflows/_dft.py +++ b/src/koopmans/workflows/_dft.py @@ -122,55 +122,49 @@ def _run(self): self.print('DFT bandstructure workflow', style='heading') - if self.parameters.from_scratch: - path = Path('dft_bands') - if path.exists(): - shutil.rmtree(path) - - with utils.chdir('dft_bands'): - # First, a scf calculation - calc_scf = self.new_calculator('pw', nbnd=None) - calc_scf.prefix = 'scf' - self.run_calculator(calc_scf) - - # Second, a bands calculation - if self.parameters.calculate_bands in (True, None): - calc_bands = self.new_calculator('pw', calculation='bands', kpts=self.kpoints.path) - else: - calc_bands = self.new_calculator('pw', calculation='nscf') - calc_bands.prefix = 'bands' - self.link(calc_scf, calc_scf.parameters.outdir, calc_bands, calc_bands.parameters.outdir, symlink=True) - self.run_calculator(calc_bands) - - # Prepare the band structure for plotting - if self.parameters.calculate_bands in (True, None): - bs = calc_bands.results['band structure'] - - # Third, a PDOS calculation - pseudos = [pseudopotentials.read_pseudo_file(calc_scf.directory / calc_scf.parameters.pseudo_dir / p) for p in - self.pseudopotentials.values()] - if all([int(p['header'].get('number_of_wfc', 0)) > 0 for p in pseudos]): - calc_dos = self.new_calculator('projwfc') - self.link(calc_bands, calc_bands.parameters.outdir, calc_dos, calc_dos.parameters.outdir, symlink=True) - self.run_calculator(calc_dos) - - # Prepare the DOS for plotting - dos = copy.deepcopy(calc_dos.results['dos']) - if self.parameters.calculate_bands in (True, None): - dos._energies -= bs.reference - else: - # Skip if the pseudos don't have the requisite PP_PSWFC blocks - utils.warn('Some of the pseudopotentials do not have `PP_PSWFC` blocks, which means a projected DOS ' - 'calculation is not possible. Skipping...') - dos = None - - # Plot the band structure and DOS + # First, a scf calculation + calc_scf = self.new_calculator('pw', nbnd=None) + calc_scf.prefix = 'scf' + self.run_calculator(calc_scf) + + # Second, a bands calculation + if self.parameters.calculate_bands in (True, None): + calc_bands = self.new_calculator('pw', calculation='bands', kpts=self.kpoints.path) + else: + calc_bands = self.new_calculator('pw', calculation='nscf') + calc_bands.prefix = 'bands' + self.link(calc_scf, calc_scf.parameters.outdir, calc_bands, calc_bands.parameters.outdir, symlink=True) + self.run_calculator(calc_bands) + + # Prepare the band structure for plotting + if self.parameters.calculate_bands in (True, None): + bs = calc_bands.results['band structure'] + + # Third, a PDOS calculation + pseudos = [pseudopotentials.read_pseudo_file(calc_scf.directory / calc_scf.parameters.pseudo_dir / p) for p in + self.pseudopotentials.values()] + if all([int(p['header'].get('number_of_wfc', 0)) > 0 for p in pseudos]): + calc_dos = self.new_calculator('projwfc') + self.link(calc_bands, calc_bands.parameters.outdir, calc_dos, calc_dos.parameters.outdir, symlink=True) + self.run_calculator(calc_dos) + + # Prepare the DOS for plotting + dos = copy.deepcopy(calc_dos.results['dos']) if self.parameters.calculate_bands in (True, None): - self.plot_bandstructure(bs.subtract_reference(), dos) - elif dos is not None: - workflow_name = self.__class__.__name__.lower() - filename = f'{self.name}_{workflow_name}_dos' - dos.plot(filename=filename) + dos._energies -= bs.reference + else: + # Skip if the pseudos don't have the requisite PP_PSWFC blocks + utils.warn('Some of the pseudopotentials do not have `PP_PSWFC` blocks, which means a projected DOS ' + 'calculation is not possible. Skipping...') + dos = None + + # Plot the band structure and DOS + if self.parameters.calculate_bands in (True, None): + self.plot_bandstructure(bs.subtract_reference(), dos) + elif dos is not None: + workflow_name = self.__class__.__name__.lower() + filename = f'{self.name}_{workflow_name}_dos' + dos.plot(filename=filename) def new_calculator(self, calc_type: str, diff --git a/src/koopmans/workflows/_folding.py b/src/koopmans/workflows/_folding.py index 54e8374dc..861daa094 100644 --- a/src/koopmans/workflows/_folding.py +++ b/src/koopmans/workflows/_folding.py @@ -67,7 +67,6 @@ def _run(self): pass # Link the input files - assert isinstance(calc_w2k, utils.HasDirectoryAttr) self.link(*self._hr_files[block.name], calc_w2k, self._hr_files[block.name].name, symlink=True) self.link(*self._nscf_outdir, calc_w2k, calc_w2k.parameters.outdir, recursive_symlink=True) self.link(w90_pp_calc, w90_pp_calc.prefix + '.nnkp', calc_w2k, diff --git a/src/koopmans/workflows/_koopmans_dscf.py b/src/koopmans/workflows/_koopmans_dscf.py index 07498bef1..f376dbd84 100644 --- a/src/koopmans/workflows/_koopmans_dscf.py +++ b/src/koopmans/workflows/_koopmans_dscf.py @@ -475,7 +475,7 @@ def _run(self): # Link the temporary files from the previous calculation previous_calc = self._previous_n_electron_calculation - assert isinstance(previous_calc, utils.HasDirectoryAttr) + assert isinstance(previous_calc, utils.HasDirectoryInfo) self.link(previous_calc, previous_calc.write_directory, trial_calc, trial_calc.read_directory, recursive_symlink=True) diff --git a/src/koopmans/workflows/_workflow.py b/src/koopmans/workflows/_workflow.py index a16bbc3cf..f1455ca1f 100644 --- a/src/koopmans/workflows/_workflow.py +++ b/src/koopmans/workflows/_workflow.py @@ -114,6 +114,7 @@ class Workflow(ABC): snapshots: List[Atoms] version: str _step_counter: int + _base_directory: Path | None def __init__(self, atoms: Atoms, pseudopotentials: Dict[str, str] = {}, @@ -129,6 +130,7 @@ def __init__(self, atoms: Atoms, snapshots: Optional[List[Atoms]] = None, autogenerate_settings: bool = True, version: Optional[str] = None, + parent: Optional[Workflow] = None, **kwargs: Dict[str, Any]): # Parsing parameters @@ -149,6 +151,10 @@ def __init__(self, atoms: Atoms, self.steps: List = [] self.silent = False self.print_indent = 0 + self.parent = parent + self._base_directory = None + if self.parent is None: + self.base_directory = Path() if projections is None: proj_list: List[List[Any]] @@ -259,7 +265,9 @@ def __init__(self, atoms: Atoms, else: pseudo_dir = Path.cwd() - self.parameters.pseudo_directory = pseudo_dir.resolve() + self.parameters.pseudo_directory = os.path.relpath(pseudo_dir.resolve(), self.base_directory) + elif self.parameters.pseudo_directory.is_absolute(): + self.parameters.pseudo_directory = os.path.relpath(self.parameters.pseudo_directory, self.base_directory) # For any kwargs... for key, value in kwargs.items(): @@ -278,7 +286,8 @@ def __init__(self, atoms: Atoms, if self.parameters.task != 'ui' and autogenerate_settings: # Automatically calculate nelec/nelup/neldw/etc using information contained in the pseudopotential files # and the kcp settings - nelec = nelec_from_pseudos(self.atoms, self.pseudopotentials, self.parameters.pseudo_directory) + nelec = nelec_from_pseudos(self.atoms, self.pseudopotentials, + self.base_directory / self.parameters.pseudo_directory) tot_charge = calculator_parameters['kcp'].get('tot_charge', 0) nelec -= tot_charge tot_mag = calculator_parameters['kcp'].get('tot_magnetization', nelec % 2) @@ -292,7 +301,7 @@ def __init__(self, atoms: Atoms, for i, (l, p) in enumerate(self.pseudopotentials.items()): # ASE uses absolute values; QE uses the fraction of the valence frac_mag = calculator_parameters['kcp'].pop(f'starting_magnetization({i + 1})', 0.0) - valence = valence_from_pseudo(p, self.parameters.pseudo_directory) + valence = valence_from_pseudo(p, self.base_directory / self.parameters.pseudo_directory) starting_magmoms[l] = frac_mag * valence atoms.set_initial_magnetic_moments([starting_magmoms[l] for l in labels]) elif tot_mag != 0: @@ -345,9 +354,6 @@ def __init__(self, atoms: Atoms, 'a calculator. This calculator will be ignored.') self.atoms.calc = None - # Initialize self.parent - self.parent: Optional[Workflow] = None - # Adding excluded_bands info to self.projections if self.projections: for spin in ['up', 'down', None]: @@ -366,6 +372,9 @@ def __init__(self, atoms: Atoms, # Initialize the step counter self._step_counter = 0 + # Initialize the directories + self._directory: Path | None = None + def __eq__(self, other: Any): if isinstance(other, Workflow): return self.__dict__ == other.__dict__ @@ -387,6 +396,45 @@ def __repr__(self): entries.append(f'pseudopotentials={self.pseudopotentials}') return f'{self.__class__.__name__}(' + ',\n '.join(entries) + ')' + @property + def base_directory(self) -> Path: + if self.parent is not None: + return self.parent.base_directory + else: + if self._base_directory is None: + raise ValueError(f'{self.__class__.__name__}.base_directory has not been set') + return self._base_directory + + @base_directory.setter + def base_directory(self, value: Path): + if self.parent is not None: + raise ValueError(f'{self.__class__.__name__}.base_directory should not be set for subworkflows') + + # If the pseudo_directory has been set, we need to update it too (because it is stored relative to base_directory) + if self.parameters.pseudo_directory is not None and self._base_directory is not None: + abs_pseudo_dir = (self._base_directory / self.parameters.pseudo_directory).resolve() + assert abs_pseudo_dir.is_dir() + self.parameters.pseudo_directory = os.path.relpath(abs_pseudo_dir, value.resolve()) + + self._base_directory = value.resolve() + + @property + def directory(self) -> Path: + if self.parent is None: + return Path() + elif self._directory is None: + raise ValueError(f'{self.__class__.__name__}.directory has not been set') + return self._directory + + @directory.setter + def directory(self, value: Path): + if value.is_absolute(): + raise ValueError( + f'{self.__class__.__name__} directory must be relative to the {self.__class__.__name__},base directory') + if len(value.parents) > 1: + raise ValueError(f'{self.__class__.__name__}.directory should not be a nested directory') + self._directory = value + def run(self, subdirectory: Optional[str] = None, from_scratch: Optional[bool] = None) -> None: ''' Run the workflow @@ -408,9 +456,11 @@ def run(self, subdirectory: Optional[str] = None, from_scratch: Optional[bool] = self._run() else: if subdirectory: + self.base_directory = Path(subdirectory).resolve() with utils.chdir(subdirectory): self._run() else: + self.base_directory = Path.cwd().resolve() self._run() self.print_conclusion() @@ -435,6 +485,41 @@ def pseudopotentials(self) -> Dict[str, str]: def pseudopotentials(self, value: Dict[str, str]): self._pseudopotentials = value + def get_step_by_uuid(self, uuid: str): + for step in self.steps: + if step.uuid == uuid: + return step + raise ValueError(f'No step with UUID {uuid} found in workflow') + + @classmethod + def from_other(cls: Type[W], other_wf: Workflow, **kwargs: Any) -> W: + ''' + Creates a new workflow from another workflow, copying all settings and parameters + e.g. + >>> new_wf = Workflow.fromother(other_wf) + ''' + + parameters = copy.deepcopy(other_wf.parameters) + + # Pass the pseudo_directory as an absolute path + if 'pseudo_directory' in parameters: + parameters['pseudo_directory'] = other_wf.base_directory / parameters['pseudo_directory'] + + for k in list(kwargs): + if parameters.is_valid(k): + parameters[k] = kwargs.pop(k) + kwargs.update(**dict(atoms=copy.deepcopy(other_wf.atoms), + parameters=parameters, + calculator_parameters=copy.deepcopy(other_wf.calculator_parameters), + pseudopotentials=copy.deepcopy(other_wf.pseudopotentials), + kpoints=copy.deepcopy(other_wf.kpoints), + projections=other_wf.projections, + plotting=copy.deepcopy(other_wf.plotting), + ml=copy.deepcopy(other_wf.ml), + ml_model=other_wf.ml_model)) + + return cls(**kwargs) + @classmethod def fromparent(cls: Type[W], parent_wf: Workflow, **kwargs: Any) -> W: ''' @@ -442,24 +527,7 @@ def fromparent(cls: Type[W], parent_wf: Workflow, **kwargs: Any) -> W: e.g. >>> sub_wf = Workflow.fromparent(self) ''' - - parameters = copy.deepcopy(parent_wf.parameters) - parameter_kwargs = {k: v for k, v in kwargs.items() if parameters.is_valid(k)} - wf_kwargs = dict(atoms=copy.deepcopy(parent_wf.atoms), - parameters=parameters, - calculator_parameters=copy.deepcopy(parent_wf.calculator_parameters), - pseudopotentials=copy.deepcopy(parent_wf.pseudopotentials), - kpoints=copy.deepcopy(parent_wf.kpoints), - projections=parent_wf.projections, - plotting=copy.deepcopy(parent_wf.plotting), - ml=copy.deepcopy(parent_wf.ml), - ml_model=parent_wf.ml_model) - wf_kwargs.update(**{k: v for k, v in kwargs.items() if not parameters.is_valid(k)}) - parameters.update(**parameter_kwargs) - - child_wf = cls(**wf_kwargs) - child_wf.parent = parent_wf - return child_wf + return cls.from_other(other_wf=parent_wf, parent=parent_wf, **kwargs) def _run_sanity_checks(self): # Check internal consistency of workflow settings @@ -566,13 +634,13 @@ def _run_sanity_checks(self): self.calculator_parameters['kcp'].do_wf_cmplx = True # Check pseudopotentials exist - if not os.path.isdir(self.parameters.pseudo_directory): + if not os.path.isdir(self.base_directory / self.parameters.pseudo_directory): raise NotADirectoryError( - f'The pseudopotential directory you provided (`{self.parameters.pseudo_directory}`) does not exist') + f'The pseudopotential directory you provided (`{self.base_directory / self.parameters.pseudo_directory}`) does not exist') if self.parameters.task != 'ui': for pseudo in self.pseudopotentials.values(): - if not (self.parameters.pseudo_directory / pseudo).exists(): - raise FileNotFoundError(f'`{self.parameters.pseudo_directory / pseudo}` does not exist. Please ' + if not (self.base_directory / self.parameters.pseudo_directory / pseudo).exists(): + raise FileNotFoundError(f'`{self.base_directory / self.parameters.pseudo_directory / pseudo}` does not exist. Please ' 'double-check your pseudopotential settings') # Make sanity checks for the ML model @@ -674,7 +742,7 @@ def new_calculator(self, raise ValueError(f'Cound not find a calculator of type `{calc_type}`') # Merge calculator_parameters and kwargs, giving kwargs higher precedence - all_kwargs: Dict[str, Any] = {} + all_kwargs: Dict[str, Any] = {'parent': self} calculator_parameters = self.calculator_parameters[calc_type] all_kwargs.update(**calculator_parameters) all_kwargs.update(**kwargs) @@ -710,7 +778,8 @@ def new_calculator(self, # Link the pseudopotentials if relevant if calculator_parameters.is_valid('pseudo_dir'): for pseudo in self.pseudopotentials.values(): - self.link(None, self.parameters.pseudo_directory / pseudo, calc, Path('pseudopotentials') / pseudo) + self.link(None, self.base_directory / self.parameters.pseudo_directory / + pseudo, calc, Path('pseudopotentials') / pseudo) calc.parameters.pseudo_dir = 'pseudopotentials' return calc @@ -834,16 +903,16 @@ def _pre_run_calculator(self, qe_calc: calculators.Calc) -> bool: # Check that calc.directory was not set if qe_calc.directory is not None: raise ValueError( - f'`calc.directory` should not be set manually, but it was set to `{os.path.relpath(qe_calc.directory)}`') + f'`calc.directory` should not be set manually, but it was set to `{qe_calc.directory}`') # Prepend calc.directory with a counter self._step_counter += 1 - qe_calc.directory = Path(f'{self._step_counter:02}-{qe_calc.prefix}').resolve() + qe_calc.directory = Path(f'{self._step_counter:02}-{qe_calc.prefix}') # Check that another calculation hasn't already been run in this directory - if any([calc.directory == qe_calc.directory for calc in self.calculations]): + if any([calc.absolute_directory == qe_calc.absolute_directory for calc in self.calculations]): raise ValueError( - f'A calculation has already been run in `{os.path.relpath(qe_calc.directory)}`; this should not happen') + f'A calculation has already been run in `{qe_calc.directory}`; this should not happen') # If an output file already exists, check if the run completed successfully if not self.parameters.from_scratch: @@ -934,6 +1003,7 @@ def run_calculators(self, calcs: List[calculators.Calc]): calcs_to_run = [] for calc in calcs: + calc.parent = self proceed = self._pre_run_calculator(calc) if proceed: calcs_to_run.append(calc) @@ -948,8 +1018,9 @@ def run_process(self, process: Process): Run a Process ''' + process.parent = self self._step_counter += 1 - process.directory = Path(f'{self._step_counter:02}-{process.name}').resolve() + process.directory = Path(f'{self._step_counter:02}-{process.name}') if not self.parameters.from_scratch and process.is_complete(): self.print(f'- ⏭️ Not running `{os.path.relpath(process.directory)}` as it is already complete ') @@ -980,7 +1051,7 @@ def load_old_calculator(self, qe_calc: calculators.Calc) -> bool: return old_calc.is_complete() - def link(self, src_calc: utils.HasDirectoryAttr | None, src_path: Path | str, dest_calc: calculators.Calc, dest_path: Path | str, symlink=False, recursive_symlink=False, overwrite=False) -> None: + def link(self, src_calc: utils.HasDirectoryInfo | None, src_path: Path | str, dest_calc: calculators.Calc, dest_path: Path | str, symlink=False, recursive_symlink=False, overwrite=False) -> None: """Link a file from one calculator to another Paths must be provided relative to the the calculator's directory i.e. calc.directory, unless src_calc is None @@ -1009,6 +1080,9 @@ def link(self, src_calc: utils.HasDirectoryAttr | None, src_path: Path | str, de if src_path.is_absolute() and src_calc is not None: raise ValueError(f'`src_path` in `{self.__class__.__name__}.link()` must be a relative path if a ' f'`src_calc` is provided') + if src_calc is None and not src_path.is_absolute(): + raise ValueError( + f'`src_path` in `{self.__class__.__name__}.link()` must be an absolute path if `src_calc` is not provided') if dest_path.is_absolute(): raise ValueError(f'`dest_path` in `{self.__class__.__name__}.link()` must be a relative path') @@ -1071,16 +1145,9 @@ def _parent_context(self, subdirectory: Optional[str] = None, subdirectory_path = Path(f'{self.parent._step_counter:02}-{subdirectory}') if self.parameters.from_scratch and subdirectory_path.is_dir(): shutil.rmtree(subdirectory_path) - # Update directories - for key in self.calculator_parameters.keys(): - params = self.calculator_parameters[key] - for setting in params.are_paths: - if setting == 'pseudo_dir': - continue - path = getattr(params, setting, None) - if path is not None and Path.cwd() in path.parents: - new_path = subdirectory_path.resolve() / os.path.relpath(path) - setattr(params, setting, new_path) + + # Store the directory + self.directory = subdirectory_path # Run the workflow with utils.chdir(subdirectory_path): @@ -1591,7 +1658,8 @@ def _teardown(self): def number_of_electrons(self, spin: Optional[str] = None) -> int: # Return the number of electrons in a particular spin channel - nelec_tot = nelec_from_pseudos(self.atoms, self.pseudopotentials, self.parameters.pseudo_directory) + nelec_tot = nelec_from_pseudos(self.atoms, self.pseudopotentials, + self.base_directory / self.parameters.pseudo_directory) pw_params = self.calculator_parameters['pw'] if self.parameters.spin_polarized: nelec = nelec_tot - pw_params.get('tot_charge', 0) diff --git a/tests/benchmarks/test_compute_power_spectrum_pr0/compute_power_spectrum.pkl b/tests/benchmarks/test_compute_power_spectrum_pr0/compute_power_spectrum.pkl index 3bddc3885..2aa05a4fb 100644 Binary files a/tests/benchmarks/test_compute_power_spectrum_pr0/compute_power_spectrum.pkl and b/tests/benchmarks/test_compute_power_spectrum_pr0/compute_power_spectrum.pkl differ diff --git a/tests/benchmarks/test_convergence_h2o0/01-dftcp-ecutwfc-20_0-celldm1-18_9/01-dft_nspin1/dft_nspin1.pkl b/tests/benchmarks/test_convergence_h2o0/01-dftcp-ecutwfc-20_0-celldm1-18_9/01-dft_nspin1/dft_nspin1.pkl index 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a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/01-kipz_nspin1_dummy/kipz_nspin1_dummy.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/01-kipz_nspin1_dummy/kipz_nspin1_dummy.pkl index 0947ecdbb..037470135 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/01-kipz_nspin1_dummy/kipz_nspin1_dummy.pkl and b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/01-kipz_nspin1_dummy/kipz_nspin1_dummy.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/02-convert_files_from_spin2to1/convert_files_from_spin2to1.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/02-convert_files_from_spin2to1/convert_files_from_spin2to1.pkl 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differ diff --git a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/04-kipz_nspin2_dummy/kipz_nspin2_dummy.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/04-kipz_nspin2_dummy/kipz_nspin2_dummy.pkl index cb7f540cd..b308d4ccc 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/04-kipz_nspin2_dummy/kipz_nspin2_dummy.pkl and b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/04-kipz_nspin2_dummy/kipz_nspin2_dummy.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/05-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/05-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl index 65542a5f0..ee8ee7e99 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/05-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl and b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/05-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/06-kipz_nspin2/kipz_nspin2.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/06-kipz_nspin2/kipz_nspin2.pkl index e8572d2fc..d4d5f8457 100644 Binary files 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a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/08-orbital-5/02-kipz_n+1/kipz_n+1.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/08-orbital-5/02-kipz_n+1/kipz_n+1.pkl index 10b446a39..0b9d6f45e 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/08-orbital-5/02-kipz_n+1/kipz_n+1.pkl and b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/01-calculate-screening-via-dscf/02-iteration-2/08-orbital-5/02-kipz_n+1/kipz_n+1.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/02-kipz_final/kipz_final.pkl b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/02-kipz_final/kipz_final.pkl index 27ec0abf6..380e2ce48 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/02-kipz_final/kipz_final.pkl and b/tests/benchmarks/test_singlepoint_h2o_all_dscf0/03-kipz/02-kipz_final/kipz_final.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl index bd36dcdd9..fce7167fb 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl index f1bcd3ddb..089c4eb1c 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl index 0ce2246e3..6f2df5468 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/04-dft_init_nspin2/dft_init_nspin2.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/04-dft_init_nspin2/dft_init_nspin2.pkl index 3e33f78f1..1cd17f3d0 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/04-dft_init_nspin2/dft_init_nspin2.pkl and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/04-dft_init_nspin2/dft_init_nspin2.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/05-pz_innerloop_init/pz_innerloop_init.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/05-pz_innerloop_init/pz_innerloop_init.pkl index 45d665a98..bed1f59c6 100644 Binary files a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/05-pz_innerloop_init/pz_innerloop_init.pkl and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-initialization/05-pz_innerloop_init/pz_innerloop_init.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl new file mode 100644 index 000000000..696a0d17b Binary files /dev/null and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1_metadata.json b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1_metadata.json new file mode 100644 index 000000000..61536be64 --- /dev/null +++ b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/01-dft_init_nspin1/dft_init_nspin1_metadata.json @@ -0,0 +1 @@ +{"input_files": ["pseudopotentials/H_ONCV_PBE-1.2.upf", "pseudopotentials/O_ONCV_PBE-1.2.upf"], "output_files": ["TMP-CP/kc.cel", "TMP-CP/kc.con", "TMP-CP/kc.eig", "TMP-CP/kc.evp", "TMP-CP/kc.for", "TMP-CP/kc.ham", "TMP-CP/kc.nos", "TMP-CP/kc.ovp", "TMP-CP/kc.pol", "TMP-CP/kc.pos", "TMP-CP/kc.sha", "TMP-CP/kc.spr", "TMP-CP/kc.str", "TMP-CP/kc.the", "TMP-CP/kc.vel", "TMP-CP/kc.wfc", "TMP-CP/kc_98.save/H_ONCV_PBE-1.2.upf", "TMP-CP/kc_98.save/K00001/eigenval.xml", "TMP-CP/kc_98.save/K00001/evc.dat", "TMP-CP/kc_98.save/K00001/evc0.dat", "TMP-CP/kc_98.save/K00001/evc0_empty1.dat", "TMP-CP/kc_98.save/K00001/evc_empty1.dat", "TMP-CP/kc_98.save/K00001/evcm.dat", "TMP-CP/kc_98.save/K00001/gkvectors.dat", "TMP-CP/kc_98.save/K00001/hamiltonian.xml", "TMP-CP/kc_98.save/K00001/hamiltonian_emp.xml", "TMP-CP/kc_98.save/K00001/lambda01.dat", "TMP-CP/kc_98.save/K00001/lambdam1.dat", "TMP-CP/kc_98.save/O_ONCV_PBE-1.2.upf", "TMP-CP/kc_98.save/charge-density.dat", "TMP-CP/kc_98.save/data-file.xml", "TMP-CP/kc_98.save/gvectors.dat", "TMP-CP/kc_98.save/print_counter.xml", "dft_init_nspin1.cpo", "dft_init_nspin1.ham.pkl"]} \ No newline at end of file diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl new file mode 100644 index 000000000..9cbff0b1e Binary files /dev/null and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy.pkl differ diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy_metadata.json b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy_metadata.json new file mode 100644 index 000000000..b96d772ce --- /dev/null +++ b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/02-dft_init_nspin2_dummy/dft_init_nspin2_dummy_metadata.json @@ -0,0 +1 @@ +{"input_files": ["pseudopotentials/H_ONCV_PBE-1.2.upf", "pseudopotentials/O_ONCV_PBE-1.2.upf"], "output_files": ["TMP-CP/kc.cel", "TMP-CP/kc.con", "TMP-CP/kc.eig", "TMP-CP/kc.evp", "TMP-CP/kc.for", "TMP-CP/kc.ham", "TMP-CP/kc.nos", "TMP-CP/kc.ovp", "TMP-CP/kc.pol", "TMP-CP/kc.pos", "TMP-CP/kc.sha", "TMP-CP/kc.spr", "TMP-CP/kc.str", "TMP-CP/kc.the", "TMP-CP/kc.vel", "TMP-CP/kc.wfc", "TMP-CP/kc_99.save/H_ONCV_PBE-1.2.upf", "TMP-CP/kc_99.save/K00001/eigenval1.xml", "TMP-CP/kc_99.save/K00001/eigenval2.xml", "TMP-CP/kc_99.save/K00001/evc01.dat", "TMP-CP/kc_99.save/K00001/evc02.dat", "TMP-CP/kc_99.save/K00001/evc0_empty1.dat", "TMP-CP/kc_99.save/K00001/evc0_empty2.dat", "TMP-CP/kc_99.save/K00001/evc1.dat", "TMP-CP/kc_99.save/K00001/evc2.dat", "TMP-CP/kc_99.save/K00001/evc_empty1.dat", "TMP-CP/kc_99.save/K00001/evc_empty2.dat", "TMP-CP/kc_99.save/K00001/evcm1.dat", "TMP-CP/kc_99.save/K00001/evcm2.dat", "TMP-CP/kc_99.save/K00001/gkvectors.dat", "TMP-CP/kc_99.save/K00001/hamiltonian1.xml", "TMP-CP/kc_99.save/K00001/hamiltonian2.xml", "TMP-CP/kc_99.save/K00001/hamiltonian_emp1.xml", "TMP-CP/kc_99.save/K00001/hamiltonian_emp2.xml", "TMP-CP/kc_99.save/K00001/lambda01.dat", "TMP-CP/kc_99.save/K00001/lambda02.dat", "TMP-CP/kc_99.save/K00001/lambdam1.dat", "TMP-CP/kc_99.save/K00001/lambdam2.dat", "TMP-CP/kc_99.save/O_ONCV_PBE-1.2.upf", "TMP-CP/kc_99.save/charge-density.dat", "TMP-CP/kc_99.save/data-file.xml", "TMP-CP/kc_99.save/gvectors.dat", "TMP-CP/kc_99.save/print_counter.xml", "TMP-CP/kc_99.save/spin-polarization.dat", "dft_init_nspin2_dummy.cpo", "dft_init_nspin2_dummy.ham.pkl"]} \ No newline at end of file diff --git a/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl new file mode 100644 index 000000000..e4a92bcb1 Binary files /dev/null and b/tests/benchmarks/test_singlepoint_h2o_ki_dscf_e0/01-koopmans-dscf/01-koopmans-dscf/01-initialization/03-convert_files_from_spin1to2/convert_files_from_spin1to2.pkl differ diff 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b/tests/benchmarks/tutorials/tutorial_2/test_run_ki/01-koopmans-dscf/02-calculate-screening-via-dscf/01-iteration-1/03-orbital-33/01-dft_n+1_dummy/dft_n+1_dummy_metadata.json new file mode 100644 index 000000000..7b2351abc --- /dev/null +++ b/tests/benchmarks/tutorials/tutorial_2/test_run_ki/01-koopmans-dscf/02-calculate-screening-via-dscf/01-iteration-1/03-orbital-33/01-dft_n+1_dummy/dft_n+1_dummy_metadata.json @@ -0,0 +1 @@ +{"input_files": ["pseudopotentials/Si.upf"], "output_files": ["TMP-CP/kc.cel", "TMP-CP/kc.con", "TMP-CP/kc.eig", "TMP-CP/kc.evp", "TMP-CP/kc.for", "TMP-CP/kc.ham", "TMP-CP/kc.nos", "TMP-CP/kc.ovp", "TMP-CP/kc.pol", "TMP-CP/kc.pos", "TMP-CP/kc.sha", "TMP-CP/kc.spr", "TMP-CP/kc.str", "TMP-CP/kc.the", "TMP-CP/kc.vel", "TMP-CP/kc.wfc", "TMP-CP/kc_65.save/K00001/eigenval1.xml", "TMP-CP/kc_65.save/K00001/eigenval2.xml", "TMP-CP/kc_65.save/K00001/evc01.dat", "TMP-CP/kc_65.save/K00001/evc02.dat", "TMP-CP/kc_65.save/K00001/evc1.dat", "TMP-CP/kc_65.save/K00001/evc2.dat", 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7b1f21584..000000000 Binary files a/tests/benchmarks/tutorials/tutorial_3/dft_bands/01-scf/scf.pkl and /dev/null differ diff --git a/tests/benchmarks/tutorials/tutorial_3/dft_bands/01-scf/scf_metadata.json b/tests/benchmarks/tutorials/tutorial_3/dft_bands/01-scf/scf_metadata.json deleted file mode 100644 index 9f2560ad0..000000000 --- a/tests/benchmarks/tutorials/tutorial_3/dft_bands/01-scf/scf_metadata.json +++ /dev/null @@ -1 +0,0 @@ -{"input_files": ["pseudopotentials/O.upf", "pseudopotentials/Zn.upf"], "output_files": ["TMP/kc.save/O.upf", "TMP/kc.save/Zn.upf", "TMP/kc.save/charge-density.dat", "TMP/kc.save/data-file-schema.xml", "TMP/kc.save/wfc1.dat", "TMP/kc.save/wfc10.dat", "TMP/kc.save/wfc11.dat", "TMP/kc.save/wfc12.dat", "TMP/kc.save/wfc13.dat", "TMP/kc.save/wfc14.dat", "TMP/kc.save/wfc15.dat", "TMP/kc.save/wfc16.dat", "TMP/kc.save/wfc17.dat", "TMP/kc.save/wfc18.dat", "TMP/kc.save/wfc19.dat", "TMP/kc.save/wfc2.dat", "TMP/kc.save/wfc20.dat", "TMP/kc.save/wfc21.dat", "TMP/kc.save/wfc3.dat", "TMP/kc.save/wfc4.dat", "TMP/kc.save/wfc5.dat", "TMP/kc.save/wfc6.dat", "TMP/kc.save/wfc7.dat", "TMP/kc.save/wfc8.dat", "TMP/kc.save/wfc9.dat", "TMP/kc.xml", "scf.pwo"]} \ No newline at end of file diff --git a/tests/benchmarks/tutorials/tutorial_3/dft_bands/02-bands/bands.pkl b/tests/benchmarks/tutorials/tutorial_3/dft_bands/02-bands/bands.pkl deleted file mode 100644 index 4b215fab8..000000000 Binary files a/tests/benchmarks/tutorials/tutorial_3/dft_bands/02-bands/bands.pkl and /dev/null differ diff --git a/tests/benchmarks/tutorials/tutorial_3/dft_bands/02-bands/bands_metadata.json b/tests/benchmarks/tutorials/tutorial_3/dft_bands/02-bands/bands_metadata.json deleted file mode 100644 index 131116e63..000000000 --- a/tests/benchmarks/tutorials/tutorial_3/dft_bands/02-bands/bands_metadata.json +++ /dev/null @@ -1 +0,0 @@ -{"input_files": ["pseudopotentials/O.upf", "pseudopotentials/Zn.upf"], "output_files": ["bands.pwo"]} \ No newline at end of file diff --git a/tests/benchmarks/tutorials/tutorial_3/dft_bands/03-projwfc/projwfc.pkl b/tests/benchmarks/tutorials/tutorial_3/dft_bands/03-projwfc/projwfc.pkl deleted file mode 100644 index 3a107171f..000000000 Binary files a/tests/benchmarks/tutorials/tutorial_3/dft_bands/03-projwfc/projwfc.pkl and /dev/null differ diff --git a/tests/benchmarks/tutorials/tutorial_3/dft_bands/03-projwfc/projwfc_metadata.json b/tests/benchmarks/tutorials/tutorial_3/dft_bands/03-projwfc/projwfc_metadata.json deleted file mode 100644 index 0ae93065f..000000000 --- a/tests/benchmarks/tutorials/tutorial_3/dft_bands/03-projwfc/projwfc_metadata.json +++ /dev/null @@ -1 +0,0 @@ -{"input_files": [], "output_files": ["projwfc.pro"]} \ No newline at end of file diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/01-scf/scf.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/01-scf/scf.pkl new file mode 100644 index 000000000..73646a3da Binary 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a/tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_atm#4(O)_wfc#2(p) b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_atm#4(O)_wfc#2(p) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_atm#4(O)_wfc#2(p) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_atm#4(O)_wfc#2(p) diff --git a/tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_tot b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_tot similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_tot rename to tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/Wannierize.pdos_tot diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc.pkl new file mode 100644 index 000000000..622326135 Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc_metadata.json similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc_metadata.json rename to tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/01-wannier/12-projwfc/projwfc_metadata.json diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc.pkl new file mode 100644 index 000000000..0f3f30fb7 Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc_metadata.json similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc_metadata.json rename to tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/02-wann2kc/wann2kc_metadata.json diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham.pkl new file mode 100644 index 000000000..30c71cdbb Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham_metadata.json similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham_metadata.json rename to tests/benchmarks/tutorials/tutorial_3/test_zno_ki/dfpt/01-koopmans-dfpt/03-kc_ham/kc_ham_metadata.json diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/01-scf/scf.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/01-scf/scf.pkl new file mode 100644 index 000000000..8f805369a Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/01-scf/scf.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/01-scf/scf_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/01-scf/scf_metadata.json similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/01-scf/scf_metadata.json rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/01-scf/scf_metadata.json diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/02-bands/bands.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/02-bands/bands.pkl new file mode 100644 index 000000000..a43625b8d Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/02-bands/bands.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/02-bands/bands_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/02-bands/bands_metadata.json new file mode 100644 index 000000000..5ada16e82 --- /dev/null +++ b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/02-bands/bands_metadata.json @@ -0,0 +1 @@ +{"input_files": ["../TMP/kc.save/O.upf", "../TMP/kc.save/Zn.upf", "../TMP/kc.save/atomic_proj.xml", "../TMP/kc.save/charge-density.dat", "../TMP/kc.save/data-file-schema.xml", "../TMP/kc.save/wfc1.dat", "../TMP/kc.save/wfc10.dat", "../TMP/kc.save/wfc11.dat", "../TMP/kc.save/wfc12.dat", "../TMP/kc.save/wfc13.dat", "../TMP/kc.save/wfc14.dat", "../TMP/kc.save/wfc15.dat", "../TMP/kc.save/wfc16.dat", "../TMP/kc.save/wfc17.dat", "../TMP/kc.save/wfc18.dat", "../TMP/kc.save/wfc19.dat", "../TMP/kc.save/wfc2.dat", "../TMP/kc.save/wfc20.dat", "../TMP/kc.save/wfc21.dat", "../TMP/kc.save/wfc22.dat", "../TMP/kc.save/wfc23.dat", "../TMP/kc.save/wfc24.dat", "../TMP/kc.save/wfc25.dat", "../TMP/kc.save/wfc26.dat", "../TMP/kc.save/wfc27.dat", "../TMP/kc.save/wfc28.dat", "../TMP/kc.save/wfc29.dat", "../TMP/kc.save/wfc3.dat", "../TMP/kc.save/wfc30.dat", "../TMP/kc.save/wfc31.dat", "../TMP/kc.save/wfc32.dat", "../TMP/kc.save/wfc33.dat", "../TMP/kc.save/wfc34.dat", "../TMP/kc.save/wfc35.dat", "../TMP/kc.save/wfc36.dat", "../TMP/kc.save/wfc37.dat", "../TMP/kc.save/wfc38.dat", "../TMP/kc.save/wfc39.dat", "../TMP/kc.save/wfc4.dat", "../TMP/kc.save/wfc40.dat", "../TMP/kc.save/wfc41.dat", "../TMP/kc.save/wfc42.dat", "../TMP/kc.save/wfc43.dat", "../TMP/kc.save/wfc44.dat", "../TMP/kc.save/wfc45.dat", "../TMP/kc.save/wfc46.dat", "../TMP/kc.save/wfc47.dat", "../TMP/kc.save/wfc48.dat", "../TMP/kc.save/wfc49.dat", "../TMP/kc.save/wfc5.dat", "../TMP/kc.save/wfc50.dat", "../TMP/kc.save/wfc51.dat", "../TMP/kc.save/wfc52.dat", "../TMP/kc.save/wfc53.dat", "../TMP/kc.save/wfc54.dat", "../TMP/kc.save/wfc55.dat", "../TMP/kc.save/wfc56.dat", "../TMP/kc.save/wfc57.dat", "../TMP/kc.save/wfc58.dat", "../TMP/kc.save/wfc59.dat", "../TMP/kc.save/wfc6.dat", "../TMP/kc.save/wfc60.dat", "../TMP/kc.save/wfc61.dat", "../TMP/kc.save/wfc62.dat", "../TMP/kc.save/wfc63.dat", "../TMP/kc.save/wfc64.dat", "../TMP/kc.save/wfc7.dat", "../TMP/kc.save/wfc8.dat", "../TMP/kc.save/wfc9.dat", "../TMP/kc.xml", "../TMP/kc_bands.save/O.upf", "../TMP/kc_bands.save/Zn.upf", "../TMP/kc_bands.save/atomic_proj.xml", "../TMP/kc_bands.save/charge-density.dat", "../TMP/kc_bands.save/data-file-schema.xml", "../TMP/kc_bands.save/wfc1.dat", "../TMP/kc_bands.save/wfc10.dat", "../TMP/kc_bands.save/wfc11.dat", "../TMP/kc_bands.save/wfc12.dat", "../TMP/kc_bands.save/wfc13.dat", "../TMP/kc_bands.save/wfc14.dat", "../TMP/kc_bands.save/wfc15.dat", "../TMP/kc_bands.save/wfc16.dat", "../TMP/kc_bands.save/wfc17.dat", "../TMP/kc_bands.save/wfc18.dat", "../TMP/kc_bands.save/wfc19.dat", "../TMP/kc_bands.save/wfc2.dat", "../TMP/kc_bands.save/wfc20.dat", "../TMP/kc_bands.save/wfc21.dat", "../TMP/kc_bands.save/wfc22.dat", "../TMP/kc_bands.save/wfc23.dat", "../TMP/kc_bands.save/wfc24.dat", "../TMP/kc_bands.save/wfc25.dat", "../TMP/kc_bands.save/wfc26.dat", "../TMP/kc_bands.save/wfc27.dat", "../TMP/kc_bands.save/wfc28.dat", "../TMP/kc_bands.save/wfc29.dat", "../TMP/kc_bands.save/wfc3.dat", "../TMP/kc_bands.save/wfc30.dat", "../TMP/kc_bands.save/wfc31.dat", "../TMP/kc_bands.save/wfc32.dat", "../TMP/kc_bands.save/wfc33.dat", "../TMP/kc_bands.save/wfc34.dat", "../TMP/kc_bands.save/wfc35.dat", "../TMP/kc_bands.save/wfc36.dat", "../TMP/kc_bands.save/wfc37.dat", "../TMP/kc_bands.save/wfc38.dat", "../TMP/kc_bands.save/wfc39.dat", "../TMP/kc_bands.save/wfc4.dat", "../TMP/kc_bands.save/wfc40.dat", "../TMP/kc_bands.save/wfc41.dat", "../TMP/kc_bands.save/wfc42.dat", "../TMP/kc_bands.save/wfc43.dat", "../TMP/kc_bands.save/wfc44.dat", "../TMP/kc_bands.save/wfc45.dat", "../TMP/kc_bands.save/wfc46.dat", "../TMP/kc_bands.save/wfc47.dat", "../TMP/kc_bands.save/wfc48.dat", "../TMP/kc_bands.save/wfc49.dat", "../TMP/kc_bands.save/wfc5.dat", "../TMP/kc_bands.save/wfc50.dat", "../TMP/kc_bands.save/wfc51.dat", "../TMP/kc_bands.save/wfc52.dat", "../TMP/kc_bands.save/wfc53.dat", "../TMP/kc_bands.save/wfc54.dat", "../TMP/kc_bands.save/wfc55.dat", "../TMP/kc_bands.save/wfc56.dat", "../TMP/kc_bands.save/wfc57.dat", "../TMP/kc_bands.save/wfc58.dat", "../TMP/kc_bands.save/wfc59.dat", "../TMP/kc_bands.save/wfc6.dat", "../TMP/kc_bands.save/wfc60.dat", "../TMP/kc_bands.save/wfc61.dat", "../TMP/kc_bands.save/wfc62.dat", "../TMP/kc_bands.save/wfc63.dat", "../TMP/kc_bands.save/wfc64.dat", "../TMP/kc_bands.save/wfc7.dat", "../TMP/kc_bands.save/wfc8.dat", "../TMP/kc_bands.save/wfc9.dat", "../TMP/kc_bands.xml", "pseudopotentials/O.upf", "pseudopotentials/Zn.upf"], "output_files": ["bands.pwo"]} \ No newline at end of file diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/projwfc.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/projwfc.pkl new file mode 100644 index 000000000..74d5f9998 Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/projwfc.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/projwfc_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/projwfc_metadata.json new file mode 100644 index 000000000..7ce3389fd --- /dev/null +++ b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/projwfc_metadata.json @@ -0,0 +1 @@ +{"input_files": ["../TMP/kc.save/O.upf", "../TMP/kc.save/Zn.upf", "../TMP/kc.save/atomic_proj.xml", "../TMP/kc.save/charge-density.dat", "../TMP/kc.save/data-file-schema.xml", "../TMP/kc.save/wfc1.dat", "../TMP/kc.save/wfc10.dat", "../TMP/kc.save/wfc11.dat", "../TMP/kc.save/wfc12.dat", "../TMP/kc.save/wfc13.dat", "../TMP/kc.save/wfc14.dat", "../TMP/kc.save/wfc15.dat", "../TMP/kc.save/wfc16.dat", "../TMP/kc.save/wfc17.dat", "../TMP/kc.save/wfc18.dat", "../TMP/kc.save/wfc19.dat", "../TMP/kc.save/wfc2.dat", "../TMP/kc.save/wfc20.dat", "../TMP/kc.save/wfc21.dat", "../TMP/kc.save/wfc22.dat", "../TMP/kc.save/wfc23.dat", "../TMP/kc.save/wfc24.dat", "../TMP/kc.save/wfc25.dat", "../TMP/kc.save/wfc26.dat", "../TMP/kc.save/wfc27.dat", "../TMP/kc.save/wfc28.dat", "../TMP/kc.save/wfc29.dat", "../TMP/kc.save/wfc3.dat", "../TMP/kc.save/wfc30.dat", "../TMP/kc.save/wfc31.dat", "../TMP/kc.save/wfc32.dat", "../TMP/kc.save/wfc33.dat", "../TMP/kc.save/wfc34.dat", "../TMP/kc.save/wfc35.dat", "../TMP/kc.save/wfc36.dat", "../TMP/kc.save/wfc37.dat", "../TMP/kc.save/wfc38.dat", "../TMP/kc.save/wfc39.dat", "../TMP/kc.save/wfc4.dat", "../TMP/kc.save/wfc40.dat", "../TMP/kc.save/wfc41.dat", "../TMP/kc.save/wfc42.dat", "../TMP/kc.save/wfc43.dat", "../TMP/kc.save/wfc44.dat", "../TMP/kc.save/wfc45.dat", "../TMP/kc.save/wfc46.dat", "../TMP/kc.save/wfc47.dat", "../TMP/kc.save/wfc48.dat", "../TMP/kc.save/wfc49.dat", "../TMP/kc.save/wfc5.dat", "../TMP/kc.save/wfc50.dat", "../TMP/kc.save/wfc51.dat", "../TMP/kc.save/wfc52.dat", "../TMP/kc.save/wfc53.dat", "../TMP/kc.save/wfc54.dat", "../TMP/kc.save/wfc55.dat", "../TMP/kc.save/wfc56.dat", "../TMP/kc.save/wfc57.dat", "../TMP/kc.save/wfc58.dat", "../TMP/kc.save/wfc59.dat", "../TMP/kc.save/wfc6.dat", "../TMP/kc.save/wfc60.dat", "../TMP/kc.save/wfc61.dat", "../TMP/kc.save/wfc62.dat", "../TMP/kc.save/wfc63.dat", "../TMP/kc.save/wfc64.dat", "../TMP/kc.save/wfc7.dat", "../TMP/kc.save/wfc8.dat", "../TMP/kc.save/wfc9.dat", "../TMP/kc.xml", "../TMP/kc_bands.save/O.upf", "../TMP/kc_bands.save/Zn.upf", "../TMP/kc_bands.save/atomic_proj.xml", "../TMP/kc_bands.save/charge-density.dat", "../TMP/kc_bands.save/data-file-schema.xml", "../TMP/kc_bands.save/wfc1.dat", "../TMP/kc_bands.save/wfc10.dat", "../TMP/kc_bands.save/wfc11.dat", "../TMP/kc_bands.save/wfc12.dat", "../TMP/kc_bands.save/wfc13.dat", "../TMP/kc_bands.save/wfc14.dat", "../TMP/kc_bands.save/wfc15.dat", "../TMP/kc_bands.save/wfc16.dat", "../TMP/kc_bands.save/wfc17.dat", "../TMP/kc_bands.save/wfc18.dat", "../TMP/kc_bands.save/wfc19.dat", "../TMP/kc_bands.save/wfc2.dat", "../TMP/kc_bands.save/wfc20.dat", "../TMP/kc_bands.save/wfc21.dat", "../TMP/kc_bands.save/wfc22.dat", "../TMP/kc_bands.save/wfc23.dat", "../TMP/kc_bands.save/wfc24.dat", "../TMP/kc_bands.save/wfc25.dat", "../TMP/kc_bands.save/wfc26.dat", "../TMP/kc_bands.save/wfc27.dat", "../TMP/kc_bands.save/wfc28.dat", "../TMP/kc_bands.save/wfc29.dat", "../TMP/kc_bands.save/wfc3.dat", "../TMP/kc_bands.save/wfc30.dat", "../TMP/kc_bands.save/wfc31.dat", "../TMP/kc_bands.save/wfc32.dat", "../TMP/kc_bands.save/wfc33.dat", "../TMP/kc_bands.save/wfc34.dat", "../TMP/kc_bands.save/wfc35.dat", "../TMP/kc_bands.save/wfc36.dat", "../TMP/kc_bands.save/wfc37.dat", "../TMP/kc_bands.save/wfc38.dat", "../TMP/kc_bands.save/wfc39.dat", "../TMP/kc_bands.save/wfc4.dat", "../TMP/kc_bands.save/wfc40.dat", "../TMP/kc_bands.save/wfc41.dat", "../TMP/kc_bands.save/wfc42.dat", "../TMP/kc_bands.save/wfc43.dat", "../TMP/kc_bands.save/wfc44.dat", "../TMP/kc_bands.save/wfc45.dat", "../TMP/kc_bands.save/wfc46.dat", "../TMP/kc_bands.save/wfc47.dat", "../TMP/kc_bands.save/wfc48.dat", "../TMP/kc_bands.save/wfc49.dat", "../TMP/kc_bands.save/wfc5.dat", "../TMP/kc_bands.save/wfc50.dat", "../TMP/kc_bands.save/wfc51.dat", "../TMP/kc_bands.save/wfc52.dat", "../TMP/kc_bands.save/wfc53.dat", "../TMP/kc_bands.save/wfc54.dat", "../TMP/kc_bands.save/wfc55.dat", "../TMP/kc_bands.save/wfc56.dat", "../TMP/kc_bands.save/wfc57.dat", "../TMP/kc_bands.save/wfc58.dat", "../TMP/kc_bands.save/wfc59.dat", "../TMP/kc_bands.save/wfc6.dat", "../TMP/kc_bands.save/wfc60.dat", "../TMP/kc_bands.save/wfc61.dat", "../TMP/kc_bands.save/wfc62.dat", "../TMP/kc_bands.save/wfc63.dat", "../TMP/kc_bands.save/wfc64.dat", "../TMP/kc_bands.save/wfc7.dat", "../TMP/kc_bands.save/wfc8.dat", "../TMP/kc_bands.save/wfc9.dat", "../TMP/kc_bands.xml"], "output_files": ["projwfc.pro"]} \ No newline at end of file diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#1(s) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#1(s) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#1(s) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#1(s) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#2(p) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#2(p) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#2(p) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#2(p) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#3(d) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#3(d) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#3(d) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#3(d) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#4(s) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#4(s) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#1(Zn)_wfc#4(s) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#1(Zn)_wfc#4(s) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#1(s) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#1(s) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#1(s) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#1(s) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#2(p) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#2(p) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#2(p) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#2(p) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#3(d) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#3(d) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#3(d) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#3(d) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#4(s) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#4(s) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#2(Zn)_wfc#4(s) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#2(Zn)_wfc#4(s) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#3(O)_wfc#1(s) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#3(O)_wfc#1(s) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#3(O)_wfc#1(s) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#3(O)_wfc#1(s) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#3(O)_wfc#2(p) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#3(O)_wfc#2(p) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#3(O)_wfc#2(p) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#3(O)_wfc#2(p) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#4(O)_wfc#1(s) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#4(O)_wfc#1(s) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#4(O)_wfc#1(s) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#4(O)_wfc#1(s) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#4(O)_wfc#2(p) b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#4(O)_wfc#2(p) similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_atm#4(O)_wfc#2(p) rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_atm#4(O)_wfc#2(p) diff --git a/tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_tot b/tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_tot similarity index 100% rename from tests/benchmarks/tutorials/tutorial_3/09-projwfc/zno.pdos_tot rename to tests/benchmarks/tutorials/tutorial_3/test_zno_pdos/03-projwfc/zno.pdos_tot diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/01-scf/scf.pkl b/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/01-scf/scf.pkl new file mode 100644 index 000000000..284ea4fc6 Binary files /dev/null and b/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/01-scf/scf.pkl differ diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/01-scf/scf_metadata.json b/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/01-scf/scf_metadata.json new file mode 100644 index 000000000..093ad4b9f --- /dev/null +++ b/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/01-scf/scf_metadata.json @@ -0,0 +1 @@ +{"input_files": ["../TMP/kc.save/O.upf", "../TMP/kc.save/Zn.upf", "../TMP/kc.save/atomic_proj.xml", "../TMP/kc.save/charge-density.dat", "../TMP/kc.save/data-file-schema.xml", "../TMP/kc.save/wfc1.dat", "../TMP/kc.save/wfc10.dat", "../TMP/kc.save/wfc11.dat", "../TMP/kc.save/wfc12.dat", "../TMP/kc.save/wfc13.dat", "../TMP/kc.save/wfc14.dat", "../TMP/kc.save/wfc15.dat", "../TMP/kc.save/wfc16.dat", "../TMP/kc.save/wfc17.dat", "../TMP/kc.save/wfc18.dat", "../TMP/kc.save/wfc19.dat", "../TMP/kc.save/wfc2.dat", "../TMP/kc.save/wfc20.dat", "../TMP/kc.save/wfc21.dat", "../TMP/kc.save/wfc22.dat", "../TMP/kc.save/wfc23.dat", "../TMP/kc.save/wfc24.dat", "../TMP/kc.save/wfc25.dat", "../TMP/kc.save/wfc26.dat", "../TMP/kc.save/wfc27.dat", "../TMP/kc.save/wfc28.dat", "../TMP/kc.save/wfc29.dat", "../TMP/kc.save/wfc3.dat", "../TMP/kc.save/wfc30.dat", "../TMP/kc.save/wfc31.dat", "../TMP/kc.save/wfc32.dat", "../TMP/kc.save/wfc33.dat", "../TMP/kc.save/wfc34.dat", "../TMP/kc.save/wfc35.dat", "../TMP/kc.save/wfc36.dat", "../TMP/kc.save/wfc37.dat", "../TMP/kc.save/wfc38.dat", "../TMP/kc.save/wfc39.dat", "../TMP/kc.save/wfc4.dat", "../TMP/kc.save/wfc40.dat", "../TMP/kc.save/wfc41.dat", "../TMP/kc.save/wfc42.dat", "../TMP/kc.save/wfc43.dat", "../TMP/kc.save/wfc44.dat", "../TMP/kc.save/wfc45.dat", "../TMP/kc.save/wfc46.dat", "../TMP/kc.save/wfc47.dat", "../TMP/kc.save/wfc48.dat", "../TMP/kc.save/wfc49.dat", "../TMP/kc.save/wfc5.dat", "../TMP/kc.save/wfc50.dat", "../TMP/kc.save/wfc51.dat", "../TMP/kc.save/wfc52.dat", "../TMP/kc.save/wfc53.dat", "../TMP/kc.save/wfc54.dat", "../TMP/kc.save/wfc55.dat", "../TMP/kc.save/wfc56.dat", "../TMP/kc.save/wfc57.dat", "../TMP/kc.save/wfc58.dat", "../TMP/kc.save/wfc59.dat", "../TMP/kc.save/wfc6.dat", "../TMP/kc.save/wfc60.dat", "../TMP/kc.save/wfc61.dat", "../TMP/kc.save/wfc62.dat", "../TMP/kc.save/wfc63.dat", "../TMP/kc.save/wfc64.dat", "../TMP/kc.save/wfc7.dat", "../TMP/kc.save/wfc8.dat", "../TMP/kc.save/wfc9.dat", "../TMP/kc.xml", "../TMP/kc_bands.save/O.upf", "../TMP/kc_bands.save/Zn.upf", "../TMP/kc_bands.save/atomic_proj.xml", "../TMP/kc_bands.save/charge-density.dat", "../TMP/kc_bands.save/data-file-schema.xml", "../TMP/kc_bands.save/wfc1.dat", "../TMP/kc_bands.save/wfc10.dat", "../TMP/kc_bands.save/wfc11.dat", "../TMP/kc_bands.save/wfc12.dat", "../TMP/kc_bands.save/wfc13.dat", "../TMP/kc_bands.save/wfc14.dat", "../TMP/kc_bands.save/wfc15.dat", "../TMP/kc_bands.save/wfc16.dat", "../TMP/kc_bands.save/wfc17.dat", "../TMP/kc_bands.save/wfc18.dat", "../TMP/kc_bands.save/wfc19.dat", "../TMP/kc_bands.save/wfc2.dat", "../TMP/kc_bands.save/wfc20.dat", "../TMP/kc_bands.save/wfc21.dat", "../TMP/kc_bands.save/wfc22.dat", "../TMP/kc_bands.save/wfc23.dat", "../TMP/kc_bands.save/wfc24.dat", "../TMP/kc_bands.save/wfc25.dat", "../TMP/kc_bands.save/wfc26.dat", "../TMP/kc_bands.save/wfc27.dat", "../TMP/kc_bands.save/wfc28.dat", "../TMP/kc_bands.save/wfc29.dat", "../TMP/kc_bands.save/wfc3.dat", "../TMP/kc_bands.save/wfc30.dat", "../TMP/kc_bands.save/wfc31.dat", "../TMP/kc_bands.save/wfc32.dat", "../TMP/kc_bands.save/wfc33.dat", "../TMP/kc_bands.save/wfc34.dat", "../TMP/kc_bands.save/wfc35.dat", "../TMP/kc_bands.save/wfc36.dat", "../TMP/kc_bands.save/wfc37.dat", "../TMP/kc_bands.save/wfc38.dat", "../TMP/kc_bands.save/wfc39.dat", "../TMP/kc_bands.save/wfc4.dat", "../TMP/kc_bands.save/wfc40.dat", "../TMP/kc_bands.save/wfc41.dat", "../TMP/kc_bands.save/wfc42.dat", "../TMP/kc_bands.save/wfc43.dat", "../TMP/kc_bands.save/wfc44.dat", "../TMP/kc_bands.save/wfc45.dat", "../TMP/kc_bands.save/wfc46.dat", "../TMP/kc_bands.save/wfc47.dat", "../TMP/kc_bands.save/wfc48.dat", "../TMP/kc_bands.save/wfc49.dat", "../TMP/kc_bands.save/wfc5.dat", "../TMP/kc_bands.save/wfc50.dat", "../TMP/kc_bands.save/wfc51.dat", "../TMP/kc_bands.save/wfc52.dat", "../TMP/kc_bands.save/wfc53.dat", "../TMP/kc_bands.save/wfc54.dat", "../TMP/kc_bands.save/wfc55.dat", "../TMP/kc_bands.save/wfc56.dat", "../TMP/kc_bands.save/wfc57.dat", "../TMP/kc_bands.save/wfc58.dat", "../TMP/kc_bands.save/wfc59.dat", "../TMP/kc_bands.save/wfc6.dat", "../TMP/kc_bands.save/wfc60.dat", "../TMP/kc_bands.save/wfc61.dat", "../TMP/kc_bands.save/wfc62.dat", "../TMP/kc_bands.save/wfc63.dat", "../TMP/kc_bands.save/wfc64.dat", "../TMP/kc_bands.save/wfc7.dat", "../TMP/kc_bands.save/wfc8.dat", "../TMP/kc_bands.save/wfc9.dat", "../TMP/kc_bands.xml", "pseudopotentials/O.upf", "pseudopotentials/Zn.upf"], "output_files": ["TMP/kc.save/O.upf", "TMP/kc.save/Zn.upf", "TMP/kc.save/charge-density.dat", "TMP/kc.save/data-file-schema.xml", "TMP/kc.save/wfc1.dat", "TMP/kc.save/wfc10.dat", "TMP/kc.save/wfc11.dat", "TMP/kc.save/wfc12.dat", "TMP/kc.save/wfc13.dat", "TMP/kc.save/wfc14.dat", "TMP/kc.save/wfc15.dat", "TMP/kc.save/wfc16.dat", "TMP/kc.save/wfc17.dat", "TMP/kc.save/wfc18.dat", "TMP/kc.save/wfc19.dat", "TMP/kc.save/wfc2.dat", "TMP/kc.save/wfc20.dat", "TMP/kc.save/wfc21.dat", "TMP/kc.save/wfc3.dat", "TMP/kc.save/wfc4.dat", "TMP/kc.save/wfc5.dat", "TMP/kc.save/wfc6.dat", "TMP/kc.save/wfc7.dat", "TMP/kc.save/wfc8.dat", "TMP/kc.save/wfc9.dat", "TMP/kc.xml", "scf.pwo"]} \ No newline at end of file diff --git a/tests/benchmarks/tutorials/tutorial_3/test_zno_wannierize/02-nscf/nscf.pkl 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100644 --- a/tests/helpers/patches/__init__.py +++ b/tests/helpers/patches/__init__.py @@ -17,7 +17,7 @@ def path_eq(self, other): # In some cases we store paths relative to a base directory. Without knowing # the base directory, the best we can do is check that the relative path # ends the same as the absolute path - return str(self).endswith(str(other)) or str(other).endswith(str(self)) + return str(self.resolve()).endswith(str(other)) or str(other).endswith(str(self)) monkeypatch.setattr('pathlib.Path.__eq__', path_eq) diff --git a/tests/helpers/patches/_benchmark.py b/tests/helpers/patches/_benchmark.py index 0f294ee26..e801dd89d 100644 --- a/tests/helpers/patches/_benchmark.py +++ b/tests/helpers/patches/_benchmark.py @@ -10,7 +10,6 @@ ProjwfcCalculator, PW2WannierCalculator, PWCalculator, Wann2KCCalculator, Wann2KCPCalculator, Wannier90Calculator) -from koopmans.files import FilePointer from koopmans.io import write_pkl from koopmans.processes.bin2xml import Bin2XMLProcess from koopmans.processes.koopmans_cp import (ConvertFilesFromSpin1To2, @@ -35,13 +34,18 @@ def _calculate(self): # Run the calculation unpatched_calculate(self) - # Store the calculator as a pickle file to use as a benchmark + # Store the calculator as a pickle file to use as a benchmark, Temporary wiping the parent attribute so that + # the entire workflow doesn't get pickled self.results.pop('walltime', None) filename = benchmark_filename(self) if not filename.parent.exists(): filename.parent.mkdir(parents=True) - write_pkl(self, filename.name) - shutil.move(filename.name, filename) + + self.parent, parent = None, self.parent + self.linked_files, linked_files = [], self.linked_files + write_pkl(self, filename) + self.parent = parent + self.linked_files = linked_files # After running the calculation, make a new list of the files, and then work out which files have been # modified by the calculation @@ -83,15 +87,31 @@ def _run(self): filename = benchmark_filename(self) if not filename.parent.exists(): filename.parent.mkdir(parents=True) - write_pkl(self, filename.name) - shutil.move(filename.name, filename) + # Temporarily wipe the parent attribute so that the entire workflow doesn't get pickled + self.parent, parent = None, self.parent + write_pkl(self, filename) + self.parent = parent # Copy over all files that are outputs of the process that need to be read - for filepointer in recursively_find_files([o for _, o in self.outputs]): - if filepointer.name in ['power_spectrum.npy']: - shutil.copy(filepointer, benchmark_filename(self).parent / filepointer.name) + for filepath in recursively_find_files([o for _, o in self.outputs]): + if filepath.name in ['power_spectrum.npy']: + shutil.copy(filepath, benchmark_filename(self).parent / filepath.name) + + # Patching the absolute_directory property + unpatched_absolute_directory = p.absolute_directory + + def absolute_directory(self) -> Path: + if self.parent is None: + # Because we wipe parents when storing benchmarks (see above), this prevents us from being able to construct + # an absolute directory to locate files. Usually, this would raise an error. For the purposes of the test suite, + # instead simply use the base directory of the repo + return Path().resolve().relative_to(Path(__file__).parents[3]) + else: + # Default behavior + return unpatched_absolute_directory.__get__(self) monkeypatch.setattr(p, '_run', _run) + monkeypatch.setattr(p, 'absolute_directory', property(absolute_directory)) def monkeypatch_bench(monkeypatch): diff --git a/tests/helpers/patches/_mock.py b/tests/helpers/patches/_mock.py index e209c7c01..5964db700 100644 --- a/tests/helpers/patches/_mock.py +++ b/tests/helpers/patches/_mock.py @@ -9,7 +9,7 @@ from koopmans.files import FilePointer from koopmans.io import read_pkl -from koopmans.utils import chdir, symlink +from koopmans.utils import chdir, symlink, warn from ._utils import (benchmark_filename, metadata_filename, recursively_find_files) @@ -31,7 +31,7 @@ def mock_calculator__calculate(self): with chdir(self.directory): # By moving into the directory where the calculation was run, we ensure when we read in the settings that # paths are interpreted relative to this particular working directory - calc = read_pkl(benchmark_filename(self).with_suffix('.pkl')) + calc = read_pkl(benchmark_filename(self)) # Compare the settings for key in set(list(self.parameters.keys()) + list(calc.parameters.keys())): @@ -87,7 +87,8 @@ def mock_calculator__calculate(self): continue # Find the actual upf file and symlink it (so that we can read its contents if need be) - [upf_file] = [x for x in (self.directory / 'pseudopotentials').glob(filename)] + [upf_file] = [os.path.relpath(x, directory) + for x in (self.directory / 'pseudopotentials').glob(filename)] with chdir(directory): symlink(upf_file, filename) @@ -134,8 +135,9 @@ def mock_process_run(self): for f in recursively_find_files([o for _, o in self.outputs]): if f.name in ['power_spectrum.npy']: - assert (benchmark_filename(self).parent / f.name).exists() - shutil.copy(benchmark_filename(self).parent / f.name, f) + src = benchmark_filename(self).parent / f.name + assert src.exists() + shutil.copy(src, f.name) else: write_mock_file(f, self.name) diff --git a/tests/helpers/patches/_utils.py b/tests/helpers/patches/_utils.py index ddc2f296f..b457c1eda 100644 --- a/tests/helpers/patches/_utils.py +++ b/tests/helpers/patches/_utils.py @@ -1,3 +1,4 @@ +import inspect import os from pathlib import Path from typing import Set, Tuple @@ -5,18 +6,40 @@ from koopmans.files import FilePointer +def find_test_function_name(): + # Traverse the stack to locate the test function frame + for frame_info in reversed(inspect.stack()): + # Get the module where the frame was defined + module = inspect.getmodule(frame_info.frame) + if module and frame_info.function.startswith('test_'): + # Return the test function name and module path + return frame_info.function, Path(frame_info.filename) + raise ValueError('Could not find test function in the stack') + + def benchmark_filename(obj) -> Path: base_directory = Path(__file__).parents[3] benchmark_dir = base_directory / 'tests' / 'benchmarks' - assert obj.directory is not None - abs_obj_directory = obj.directory.resolve() - if base_directory / 'tests' / 'tmp' in abs_obj_directory.parents: - parent = base_directory / 'tests' / 'tmp' - else: - parent = base_directory + tests_dir = base_directory / 'tests' name = getattr(obj, 'prefix', getattr(obj, 'name', None)) assert isinstance(name, str) - benchmark_name = abs_obj_directory.relative_to(parent) / name + if tests_dir / 'tmp' in obj.absolute_directory.parents: + benchmark_name = obj.absolute_directory.relative_to(tests_dir / 'tmp') / name + else: + # This is a tutorial test, which we run in the tutorials directory. Because of this, we don't have access + # to the tmp_path automatically generated by pytest, so we need to construct something similar + + # To do so, find the top-level function that contains this test + test_function, test_file = find_test_function_name() + + # Check that the file that we found is in the tests directory + assert tests_dir in test_file.parents + relative_test_file = test_file.relative_to(tests_dir) + tutorial_dir = relative_test_file.with_name(relative_test_file.stem.replace('test_', '')) + + benchmark_name = tutorial_dir / test_function / \ + obj.absolute_directory.relative_to(base_directory / tutorial_dir) / name + return benchmark_dir / benchmark_name.with_suffix('.pkl') diff --git a/tutorials/tutorial_2/wannierize.py b/tutorials/tutorial_2/wannierize.py index 8f578c0a0..c1e4f4afc 100644 --- a/tutorials/tutorial_2/wannierize.py +++ b/tutorials/tutorial_2/wannierize.py @@ -1,14 +1,14 @@ +import shutil + from koopmans.io import read from koopmans.utils import chdir for grid_size in [2, 4, 8]: - - # Read in the input file + # Read the input file wf = read('si.json') # Modify the kgrid wf.kpoints.grid = [grid_size, grid_size, grid_size] - # Run the workflow in a subdirectory - with chdir('{0}x{0}x{0}'.format(grid_size)): - wf.run() + # Run the workflow + wf.run(subdirectory='{0}x{0}x{0}'.format(grid_size)) diff --git a/tutorials/tutorial_5/04-advanced-testing/train_and_verify.py b/tutorials/tutorial_5/04-advanced-testing/train_and_verify.py index 97bd392fd..08506cce6 100644 --- a/tutorials/tutorial_5/04-advanced-testing/train_and_verify.py +++ b/tutorials/tutorial_5/04-advanced-testing/train_and_verify.py @@ -46,21 +46,19 @@ eigenvalue_errors = [] # Run the initialization workflow (which we don't want to repeat for each model) - init_wf = InitializationWorkflow.fromparent(ab_initio_wf) + init_wf = InitializationWorkflow.from_other(ab_initio_wf) init_wf.bands = copy.deepcopy(ab_initio_wf.bands) - init_wf.parent = None init_wf.ml.train = False init_wf.run(subdirectory=f'ml/snapshot_{i_snapshot + 1}/init') descriptors = [b.power_spectrum for b in init_wf.bands.to_solve] for i_train, model in enumerate(models): # Create a Koopmans DSCF workflow, linking the outputs of the initialization workflow - ml_wf = KoopmansDSCFWorkflow.fromparent(ab_initio_wf, + ml_wf = KoopmansDSCFWorkflow.from_other(ab_initio_wf, initial_variational_orbital_files=init_wf.outputs.variational_orbital_files, previous_cp_calc=init_wf.outputs.final_calc, precomputed_descriptors=descriptors) ml_wf.bands = copy.deepcopy(ab_initio_wf.bands) - ml_wf.parent = None # Attach the model that we want to test to the workflow ml_wf.ml_model = model