├── .github └── workflows │ └── python-testing.yml ├── .gitignore ├── CHANGELOG.md ├── CITATION.cff ├── README.md ├── kgrid ├── __init__.py ├── cli.py └── series.py ├── license.md ├── setup.py └── test ├── data ├── POSCAR └── geometry.in ├── test_kgrid_cli.py ├── test_kgrid_lib.py └── test_kgrid_series_cli.py /.github/workflows/python-testing.yml: -------------------------------------------------------------------------------- 1 | # This workflow will install Python dependencies, run tests and lint with a variety of Python versions 2 | # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions 3 | 4 | name: Python testing 5 | on: 6 | push: 7 | branches: [ develop ] 8 | pull_request: 9 | branches: [ develop ] 10 | 11 | jobs: 12 | build: 13 | 14 | runs-on: ubuntu-latest 15 | strategy: 16 | matrix: 17 | python-version: [3.6, 3.9] 18 | 19 | steps: 20 | - uses: actions/checkout@v2 21 | - name: Set up Python ${{ matrix.python-version }} 22 | uses: actions/setup-python@v2 23 | with: 24 | python-version: ${{ matrix.python-version }} 25 | - name: Install package with dependencies 26 | run: | 27 | python -m pip install --upgrade pip 28 | python -m pip install flake8 pytest pytest-mock 29 | python -m pip install -e . 30 | - name: Lint with flake8 31 | run: | 32 | # stop the build if there are Python syntax errors or undefined names 33 | flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics 34 | # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide 35 | flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 36 | - name: Test with pytest 37 | run: | 38 | pytest 39 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | # Change Log 2 | 3 | Notable changes are logged here by release. This project is not 4 | expected to be especially active and follows a simplified Semantic Versioning: 5 | 6 | - Version numbers take the format X.Y 7 | - X is associated with major API breakage / changes in algorithm and results. 8 | - Y is associated with minor updates and improvements 9 | - Small amounts of code tidying, refactoring and documentation do not 10 | lead to a new release, and simply sit on the Development branch of 11 | the Git repository. 12 | 13 | The changelog format is inspired by [keep-a-changelog](https://github.com/olivierlacan/keep-a-changelog). 14 | 15 | ## [Unreleased] 16 | 17 | ## [1.2] - 2021-04-01 18 | - ASE deprecation warning cleared 19 | - Minimum ASE version specified in setup.py 20 | - This also means dropping support for Python 2.7 21 | - Introduce unit testing 22 | 23 | ### Fixed 24 | - ASE > 3.21 compatibility, backwards-compatible to ASE 3.18. 25 | 26 | ### Changed 27 | - Atoms method (`atoms.get_reciprocal_cell()`) replaced by Cell method (`atoms.cell.reciprocal()`). 28 | 29 | ## [1.1] - 2018-04-30 30 | 31 | ### Fixed 32 | - Python3 compatibility 33 | - Bug in decimal place tolerance option 34 | 35 | ### Added 36 | - Comma-separated kgrid-series output option 37 | - CASTEP-like reciprocal spacing cutoff (2 pi factor smaller than KSPACING) 38 | 39 | ### Changed 40 | - Make filename a positional argument; -f or --filename no longer needed 41 | 42 | ## [1.0] - 2016-10-07 43 | 44 | ### Changed 45 | - Correctly calculate reciprocal lattice vectors using whole 46 | cell. This is the new default behaviour. Former behaviour ("naive" 47 | apprach using only lengths of real-space cell) made available as 48 | option through Python interface and CLI. 49 | - Restructure repository for packaging with setuptools 50 | - Installation instructions in README 51 | 52 | ### Added 53 | - New emulation of VASP Auto and KSPACING modes. 54 | - Setuptools installation 55 | - New range generator for convergence testing: **kgrid-series** 56 | 57 | ## [0.2] - 2016-07-28 58 | 59 | ### Added 60 | - Present useful Python API for use with [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/) calculators 61 | 62 | ### Changed 63 | - Import routine uses [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/). This adds a 64 | dependency, but permits import of almost any major crystal structure 65 | file format. 66 | 67 | ## 0.1 - 2013-06-01 68 | 69 | ### Added 70 | - Basic codebase reading from FHI-aims input files 71 | - Optparse-based interface 72 | - GPL 73 | 74 | [Unreleased]: https://github.com/wmd-group/kgrid/compare/v1.1...HEAD 75 | [1.1]: https://github.com/wmd-group/kgrid/compare/v1.0...v1.1 76 | [1.0]: https://github.com/wmd-group/kgrid/compare/v0.2...v1.0 77 | [0.2]: https://github.com/wmd-group/kgrid/compare/v0.1...v0.2 78 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.2.0 2 | message: "Please consider citing this software as below" 3 | authors: 4 | - family-names: "Jackson" 5 | given-names: "Adam James" 6 | orcid: "https://orcid.org/0000-0001-5272-6530" 7 | title: "kgrid" 8 | version: 1.2.0 9 | date-released: 2021-04-01 10 | url: "https://github.com/wmd-group/kgrid" -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | kgrid 2 | ===== 3 | 4 | Version 1.2: [Change log](./CHANGELOG.md) 5 | 6 | Generates a suitably converged **k**-point grid for solid-state 7 | quantum chemical calculations. 8 | 9 | Current status 10 | -------------- 11 | 12 | Two programs are provided: kgrid and kgrid-series 13 | 14 | ### kgrid 15 | * The specified input file is read using Atomic Simulation Environment ([supported formats](https://wiki.fysik.dtu.dk/ase/ase/io.html#module-ase.io)) 16 | * If none is specified, looks for geometry.in (FHI-aims) in working directory 17 | * A **k**-point density is selected to satisfy a given length cutoff, 18 | as described by Moreno & Soler (1992)[1]. The length cutoff 19 | corresponds to a radius about repeated images that would be needed 20 | in a gamma-point supercell calculation to achieve the same sampling. 21 | * This **k**-point grid is expressed as a number of samples in each 22 | lattice vector and passed to standard output. (Note that this is NOT 23 | a Moreno-Soler grid as it does not use symmetry information to 24 | minimise the required number of points. It is a uniform grid 25 | specified with the same length parameter notation.) 26 | * Default **k**-point cutoff is 10Å (generally well-converged for 27 | semiconducting or insulating materials) 28 | * Optional arguments are implemented with conventional GNU/POSIX 29 | syntax, including -h help option 30 | 31 | ### kgrid-series 32 | * Reports a series of "critical" cutoffs and KSPACING values with 33 | their corresponding k-point grids. 34 | * These may be very useful for convergence testing, but users should be 35 | wary of rounding behaviour near these values. 36 | 37 | Requirements 38 | ------------ 39 | 40 | * Python 3.6 41 | * [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE) version 3.18 42 | 43 | Usage 44 | ----- 45 | 46 | ### kgrid 47 | From the command line 48 | 49 | ``` bash 50 | kgrid FILE -t TYPE -c CUTOFF 51 | ``` 52 | 53 | will return a suggested set of mesh dimensions. FILE can be any 54 | [file format supported by ASE](https://wiki.fysik.dtu.dk/ase/ase/io/io.html); 55 | if no FILE is specified, **kgrid** will look for a *geometry.in* file in 56 | the current directory. TYPE is a string specifying the format of this 57 | file; usually this argument can be left out and the correct type will 58 | be inferred by ASE. CUTOFF is the real-space cutoff parameter in Å and 59 | defaults to 10.0. 60 | 61 | There is an internal Python function which may prove useful to ASE users, with the form 62 | ``` python 63 | kgrid.calc_kpt_tuple(atoms, cutoff_length=10) 64 | ``` 65 | 66 | where `atoms` is an ASE atoms object and the function returns a 67 | tuple. As such, **kgrid** may be used while setting up a calculation 68 | with a typical ASE calculator. For example: 69 | 70 | ``` python 71 | import kgrid 72 | from ase.io import read 73 | from ase.calculators.vasp import Vasp 74 | 75 | atoms = read('my_favourite_structure.cif') 76 | calc = Vasp(xc='PBE', 77 | kpts=kgrid.calc_kpt_tuple(atoms)) 78 | atoms.set_calculator(calc) 79 | atoms.get_total_energy() 80 | ``` 81 | 82 | would perform a VASP calculation in the current directory with the PBE 83 | functional, using **kgrid** to determine the reciprocal-space sampling. 84 | 85 | ### kgrid-series 86 | 87 | ``` bash 88 | kgrid-series FILE -t TYPE --min MIN --max MAX 89 | ``` 90 | 91 | Example output: 92 | 93 | ``` bash 94 | Length cutoff KSPACING Samples 95 | ------------- -------- ------------ 96 | 10.630 0.2956 2 7 4 97 | 11.260 0.2790 2 8 4 98 | 11.860 0.2649 2 8 5 99 | 12.148 0.2586 3 8 5 100 | 13.666 0.2299 3 9 5 101 | 14.075 0.2232 3 10 5 102 | 15.185 0.2069 3 10 6 103 | 16.703 0.1881 3 11 6 104 | 16.890 0.1860 3 12 6 105 | 17.790 0.1766 3 12 7 106 | 18.222 0.1724 4 12 7 107 | 19.705 0.1594 4 13 7 108 | 19.741 0.1591 4 13 8 109 | 21.259 0.1478 4 14 8 110 | 22.520 0.1395 4 15 8 111 | 22.777 0.1379 4 15 9 112 | 23.720 0.1324 4 16 9 113 | 24.296 0.1293 5 16 9 114 | 25.335 0.1240 5 17 9 115 | 25.814 0.1217 5 17 10 116 | 27.333 0.1149 5 18 10 117 | 28.150 0.1116 5 19 10 118 | 28.852 0.1089 5 19 11 119 | 29.650 0.1060 5 20 11 120 | 121 | ``` 122 | 123 | Use the `--castep` option to replace KSPACING with "MP SPACING", which 124 | corresponds to the *KPOINTS_MP_SPACING* parameter in CASTEP 125 | (i.e. divide by 2π). 126 | 127 | INSTALLATION 128 | ------------ 129 | 130 | **kgrid** uses setuptools; from a reasonable healthy Python environment you can use 131 | 132 | pip install . 133 | 134 | with the usual pip caveats: 135 | 136 | - the `--user` flag is highly recommended and avoids the need for administrator privileges, but on a somewhat unhealthy Python installation the user packages location may not be on your paths yet. 137 | - the `-e` flag creates an "editable" installation which links to this repository and enables easy updates with git. 138 | 139 | **kgrid** is not developed on Windows but no problems are anticipated; the Anaconda Python distribution includes pip. We have had good experiences using the Windows subsystem for Linux (WSL), available on Windows 10. 140 | On Mac OSX, the system Python does not include pip but there are various ways of getting a more complete distribution such as Homebrew or Anaconda. 141 | 142 | Testing 143 | ------- 144 | 145 | To run the unit tests, install `pytest` and `pytest-mock` and run 146 | `pytest` from the project directory (i.e. the folder containing this 147 | README.) 148 | 149 | Disclaimer 150 | ---------- 151 | 152 | This program is not affiliated with ASE or any particular quantum chemistry code. 153 | This program is made available under the GNU General Public License; you are free to modify and use the code, but do so at your own risk. 154 | 155 | References 156 | ---------- 157 | 158 | [1] Moreno, J., & Soler, J. (1992). Optimal meshes for integrals in real- and reciprocal-space unit cells. *Physical Review B*, 45(24), 13891–13898. [doi:10.1103/PhysRevB.45.13891](http://dx.doi.org/10.1103/PhysRevB.45.13891) 159 | -------------------------------------------------------------------------------- /kgrid/__init__.py: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # Copyright 2016 Adam Jackson 3 | ############################################################################### 4 | # This program is free software: you can redistribute it and/or modify 5 | # it under the terms of the GNU General Public License as published by 6 | # the Free Software Foundation, either version 3 of the License, or 7 | # (at your option) any later version. 8 | # 9 | # This program is distributed in the hope that it will be useful, 10 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 11 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 12 | # GNU General Public License for more details. 13 | # 14 | # You should have received a copy of the GNU General Public License 15 | # along with this program. If not, see . 16 | ############################################################################### 17 | 18 | import numpy as np 19 | 20 | def calc_kpt_tuple(atoms, cutoff_length=10, realspace=False, mode='default'): 21 | """Calculate k-point mesh from ASE atoms object for real-space cutoff 22 | 23 | Args: 24 | :param atoms: Periodic crystal structure 25 | :type ase.atoms.Atoms 26 | :param cutoff_length: Parameter determining sample density 27 | :type float 28 | :param mode: Calculation mode; this determines the units of 29 | cutoff_length. 30 | default: Cutoff is length in Angstroms corresponding to 31 | non-overlapping radius in a hypothetical supercell 32 | (Moreno-Soler length cutoff). 33 | vasp_auto: Cutoff is length in Angstroms to be multiplied by 34 | reciprocal lattice -- equivalent to double the value used in 35 | default mode. This attempts to emulate the "fully automatic" 36 | option in a VASP k-points file. 37 | kspacing: Cutoff has units of reciprocal Angstroms and represents 38 | minimum sampling density in reciprocal space. Equivalent to 39 | 1/(2*cutoff) in default mode. This attempts to emulate the 40 | KSPACING parameter in VASP. 41 | :type str 42 | :returns: Number of samples in each reciprocal lattice vector 43 | :rtype: 3-tuple 44 | """ 45 | 46 | if mode.lower() == 'default': 47 | rounding = 'up' 48 | elif mode.lower() == 'vasp_auto': 49 | cutoff_length = (cutoff_length) / 2. 50 | rounding = 'nearest' 51 | elif mode.lower() == 'kspacing': 52 | cutoff_length = np.pi / cutoff_length 53 | rounding = 'up' 54 | elif mode.lower() == 'castep_mp_spacing': 55 | cutoff_length = 1 / (2 * cutoff_length) 56 | rounding = 'up' 57 | 58 | if realspace: 59 | return calc_kpt_tuple_naive(atoms, cutoff_length=cutoff_length, 60 | rounding=rounding) 61 | else: 62 | return calc_kpt_tuple_recip(atoms, cutoff_length=cutoff_length, 63 | rounding=rounding) 64 | 65 | 66 | def calc_kpt_tuple_naive(atoms, cutoff_length=10, rounding='up'): 67 | """Calculate k-point grid using real-space lattice vectors""" 68 | 69 | # Import lattice vectors using ASE 70 | lattice_vectors = atoms.cell 71 | 72 | # Get lattice vector magnitudes (a, b, c) according to Pythagoras' theorem 73 | abc = np.sqrt(np.sum(np.square(lattice_vectors),1)) 74 | 75 | # k-point samples required = 2*cutoff_length/(magnitude of lattice vector) 76 | k_samples = np.divide(2*cutoff_length,abc) 77 | 78 | # Rounding 79 | if rounding == 'up': 80 | k_samples = np.ceil(k_samples) 81 | else: 82 | k_samples = np.floor(k_samples + 0.5) 83 | return tuple((int(x) for x in k_samples)) 84 | 85 | 86 | def calc_kpt_tuple_recip(atoms, cutoff_length=10, rounding='up'): 87 | """Calculate reciprocal-space sampling with real-space parameter""" 88 | # Get reciprocal lattice vectors with ASE. Note that ASE does NOT include 89 | # the 2*pi factor used in many definitions of these vectors; the underlying 90 | # method is just a matrix inversoin and transposition 91 | recip_cell = atoms.cell.reciprocal() 92 | 93 | # Get reciprocal cell vector magnitudes according to Pythagoras' theorem 94 | abc_recip = np.sqrt(np.sum(np.square(recip_cell),1)) 95 | 96 | k_samples = abc_recip * 2 * cutoff_length 97 | 98 | # Rounding 99 | if rounding == 'up': 100 | k_samples = np.ceil(k_samples) 101 | else: 102 | k_samples = np.floor(k_samples + 0.5) 103 | return tuple((int(x) for x in k_samples)) 104 | 105 | -------------------------------------------------------------------------------- /kgrid/cli.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | ############################################################################### 3 | # Copyright 2016 Adam Jackson 4 | ############################################################################### 5 | # This program is free software: you can redistribute it and/or modify 6 | # it under the terms of the GNU General Public License as published by 7 | # the Free Software Foundation, either version 3 of the License, or 8 | # (at your option) any later version. 9 | # 10 | # This program is distributed in the hope that it will be useful, 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | # GNU General Public License for more details. 14 | # 15 | # You should have received a copy of the GNU General Public License 16 | # along with this program. If not, see . 17 | ############################################################################### 18 | 19 | from __future__ import print_function 20 | import ase.io 21 | from argparse import ArgumentParser 22 | from kgrid import calc_kpt_tuple 23 | 24 | def calc_grid(cutoff_length, 25 | mode='default', 26 | filename='geometry.in', 27 | filetype=False, 28 | realspace=False, 29 | pretty_print=False): 30 | 31 | if filetype: 32 | atoms = ase.io.read(filename, format=filetype) 33 | else: 34 | atoms = ase.io.read(filename) 35 | 36 | k_samples = calc_kpt_tuple( 37 | atoms, mode=mode, cutoff_length=cutoff_length, realspace=realspace) 38 | 39 | # Print vectors 40 | if pretty_print: 41 | print('{0:3.0f} {1:3.0f} {2:3.0f}'.format(*k_samples)) 42 | else: 43 | return k_samples 44 | 45 | 46 | def get_parser(): 47 | parser = ArgumentParser() 48 | parser.add_argument( 49 | action="store", 50 | nargs="?", 51 | type=str, 52 | dest="file", 53 | default="geometry.in", 54 | help="Path to input file [default: ./geometry.in]") 55 | threshold = parser.add_mutually_exclusive_group() 56 | threshold.add_argument( 57 | "-c", 58 | "--cutoff-length", 59 | action="store", 60 | type=float, 61 | dest="cutoff_length", 62 | default=10.0, 63 | help="Set length cutoff in Angstroms [default: 10]") 64 | threshold.add_argument( 65 | "-a", 66 | "--vasp-auto", 67 | action="store", 68 | type=float, 69 | dest="vasp_auto", 70 | help="Real-space cutoff like Auto in VASP KPOINTS file") 71 | threshold.add_argument( 72 | "-s", 73 | "--vasp-kspacing", 74 | action="store", 75 | type=float, 76 | dest="kspacing", 77 | help="Reciprocal-space distance like KSPACING in VASP") 78 | threshold.add_argument( 79 | "--castep", 80 | "--castep_spacing", 81 | "--castep_mp_spacing", 82 | action="store", 83 | type=float, 84 | dest="castep_mp_spacing", 85 | help=("Reciprocal-space distance like KPOINTS_MP_SPACING in CASTEP; " 86 | "this differs from Vasp-like KSPACING by factor of 1/(2 pi).")) 87 | parser.add_argument( 88 | "-t", 89 | "--type", 90 | action="store", 91 | type=str, 92 | default=False, 93 | help="Input file type. If not provided, ASE will guess.") 94 | parser.add_argument( 95 | "-r", 96 | "--realspace", 97 | action="store_true", 98 | help="Use real-space vector lengths instead of " 99 | "computing reciprocal cell; not recommended!") 100 | 101 | return parser 102 | 103 | 104 | def main(params=None): 105 | parser = get_parser() 106 | args = parser.parse_args(params) 107 | 108 | if args.vasp_auto: 109 | mode = 'vasp_auto' 110 | cutoff = args.vasp_auto 111 | elif args.kspacing: 112 | mode = 'kspacing' 113 | cutoff = args.kspacing 114 | elif args.castep_mp_spacing: 115 | mode = 'castep_mp_spacing' 116 | cutoff = args.castep_mp_spacing 117 | else: 118 | mode = 'default' 119 | cutoff = args.cutoff_length 120 | 121 | calc_grid( 122 | cutoff, 123 | mode=mode, 124 | filename=args.file, 125 | filetype=args.type, 126 | realspace=args.realspace, 127 | pretty_print=True) 128 | 129 | 130 | if __name__ == '__main__': 131 | main() 132 | -------------------------------------------------------------------------------- /kgrid/series.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | ############################################################################### 4 | # Copyright 2016 Adam Jackson 5 | ############################################################################### 6 | # This program is free software: you can redistribute it and/or modify 7 | # it under the terms of the GNU General Public License as published by 8 | # the Free Software Foundation, either version 3 of the License, or 9 | # (at your option) any later version. 10 | # 11 | # This program is distributed in the hope that it will be useful, 12 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | # GNU General Public License for more details. 15 | # 16 | # You should have received a copy of the GNU General Public License 17 | # along with this program. If not, see . 18 | ############################################################################### 19 | from __future__ import print_function 20 | 21 | import numpy as np 22 | from argparse import ArgumentParser 23 | 24 | import ase.io 25 | 26 | from kgrid import calc_kpt_tuple 27 | 28 | def get_increments(lattice_lengths): 29 | """ 30 | Calculate the vector l0 of increments between significant length cutoffs 31 | for each reciprocal lattice vector. 32 | 33 | :param lattice_lengths: Lengths of reciprocal lattice vectors 34 | :type 3-tuple 35 | 36 | :returns: Vector l0 of significant increments 37 | :rtype: 3-tuple 38 | """ 39 | 40 | return tuple([1. / (2 * a) for a in lattice_lengths]) 41 | 42 | 43 | def cutoff_series(atoms, l_min, l_max, decimals=4): 44 | """Find multiples of l0 members within a range 45 | 46 | :param atoms: Crystal structure 47 | :type ase.atoms.Atoms 48 | :param l_min: Minimum real-space cutoff 49 | :type float 50 | :param l_max: Maximum real-space cutoff 51 | :type float 52 | :param decimals: Number of decimal places used when rounding to remove 53 | duplicates 54 | :type int 55 | 56 | :returns: Sorted list of cutoffs 57 | :rtype: list 58 | """ 59 | recip_cell = atoms.cell.reciprocal() 60 | lattice_lengths = np.sqrt(np.sum(np.square(recip_cell), 1)) 61 | 62 | l0 = get_increments(lattice_lengths) 63 | 64 | members = set() 65 | for li in l0: 66 | n_min = np.ceil(l_min / li) 67 | members.update( 68 | set(np.around( 69 | np.arange(n_min * li, l_max, li), decimals=decimals))) 70 | return sorted(members) 71 | 72 | 73 | def kspacing_series(atoms, l_min, l_max, decimals=4): 74 | """Find series of KSPACING values with different results 75 | 76 | NB: It is strongly recommended to ADD a small delta to these values 77 | to account for truncation/rounding errors 78 | 79 | :param atoms: Crystal structure 80 | :type ase.atoms.Atoms 81 | :param l_min: Minimum real-space cutoff 82 | :type float 83 | :param l_max: Maximum real-space cutoff 84 | :type float 85 | 86 | :returns: Sorted list of KSPACING values 87 | :rtype: list 88 | """ 89 | 90 | return [np.pi / c for c in 91 | cutoff_series(atoms, l_min, l_max, decimals=decimals)] 92 | 93 | def get_parser(): 94 | parser = ArgumentParser("Calculate a systematic series of k-point samples") 95 | parser.add_argument( 96 | 'filename', 97 | nargs='?', 98 | type=str, 99 | default="geometry.in", 100 | help="Path to input file [default: ./geometry.in]") 101 | parser.add_argument( 102 | '-t', 103 | '--type', 104 | type=str, 105 | default=None, 106 | help='Format of crystal structure file') 107 | parser.add_argument( 108 | '--min', 109 | type=float, 110 | default=10, 111 | help='Minimum real-space cutoff / angstroms') 112 | parser.add_argument( 113 | '--max', 114 | type=float, 115 | default=30, 116 | help='Maximum real-space cutoff / angstroms') 117 | parser.add_argument('--comma_sep', action='store_true', 118 | help='Output as comma-separated list on one line') 119 | parser.add_argument('--castep', action='store_true', 120 | help=('Provide CASTEP-like MP spacing instead of ' 121 | 'vasp-like KSPACING')) 122 | return parser 123 | 124 | def main(params=None): 125 | args = get_parser().parse_args(params) 126 | 127 | if args.type: 128 | atoms = ase.io.read(args.filename, format=args.type) 129 | else: 130 | atoms = ase.io.read(args.filename) 131 | 132 | cutoffs = cutoff_series(atoms, args.min, args.max) 133 | 134 | if args.castep: 135 | kspacing = [0.5 / c for c in cutoffs] 136 | else: 137 | kspacing = [np.pi / c for c in cutoffs] 138 | 139 | samples = [calc_kpt_tuple( 140 | atoms, cutoff_length=(cutoff - 1e-4)) for cutoff in cutoffs] 141 | 142 | if args.comma_sep: 143 | def print_sample(sample): 144 | return ' '.join((str(x) for x in sample)) 145 | 146 | print(','.join((print_sample(sample) for sample in samples))) 147 | 148 | else: 149 | if args.castep: 150 | print("Length cutoff MP SPACING Samples") 151 | print("------------- ---------- ------------") 152 | fstring = "{0:12.3f} {1:9.6f} {2:3d} {3:3d} {4:3d}" 153 | else: 154 | print("Length cutoff KSPACING Samples") 155 | print("------------- -------- ------------") 156 | fstring = "{0:12.3f} {1:7.4f} {2:3d} {3:3d} {4:3d}" 157 | 158 | for cutoff, s, sample in zip(cutoffs, kspacing, samples): 159 | print(fstring.format(cutoff, s, *sample)) 160 | 161 | 162 | if __name__ == '__main__': 163 | main() 164 | -------------------------------------------------------------------------------- /license.md: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | ========================== 3 | 4 | Version 3, 29 June 2007 5 | 6 | Copyright © 2007 Free Software Foundation, Inc. <> 7 | 8 | Everyone is permitted to copy and distribute verbatim copies of this license 9 | document, but changing it is not allowed. 10 | 11 | ## Preamble 12 | 13 | The GNU General Public License is a free, copyleft license for software and other 14 | kinds of works. 15 | 16 | The licenses for most software and other practical works are designed to take away 17 | your freedom to share and change the works. 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If such problems 55 | arise substantially in other domains, we stand ready to extend this provision to 56 | those domains in future versions of the GPL, as needed to protect the freedom of 57 | users. 58 | 59 | Finally, every program is threatened constantly by software patents. States should 60 | not allow patents to restrict development and use of software on general-purpose 61 | computers, but in those that do, we wish to avoid the special danger that patents 62 | applied to a free program could make it effectively proprietary. To prevent this, the 63 | GPL assures that patents cannot be used to render the program non-free. 64 | 65 | The precise terms and conditions for copying, distribution and modification follow. 66 | 67 | ## TERMS AND CONDITIONS 68 | 69 | ### 0. Definitions. 70 | 71 | “This License” refers to version 3 of the GNU General Public License. 72 | 73 | “Copyright” also means copyright-like laws that apply to other kinds of 74 | works, such as semiconductor masks. 75 | 76 | “The Program” refers to any copyrightable work licensed under this 77 | License. Each licensee is addressed as “you”. “Licensees” and 78 | “recipients” may be individuals or organizations. 79 | 80 | To “modify” a work means to copy from or adapt all or part of the work in 81 | a fashion requiring copyright permission, other than the making of an exact copy. 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If the Program as you received 339 | it, or any part of it, contains a notice stating that it is governed by this License 340 | along with a term that is a further restriction, you may remove that term. If a 341 | license document contains a further restriction but permits relicensing or conveying 342 | under this License, you may add to a covered work material governed by the terms of 343 | that license document, provided that the further restriction does not survive such 344 | relicensing or conveying. 345 | 346 | If you add terms to a covered work in accord with this section, you must place, in 347 | the relevant source files, a statement of the additional terms that apply to those 348 | files, or a notice indicating where to find the applicable terms. 349 | 350 | Additional terms, permissive or non-permissive, may be stated in the form of a 351 | separately written license, or stated as exceptions; the above requirements apply 352 | either way. 353 | 354 | ### 8. Termination. 355 | 356 | You may not propagate or modify a covered work except as expressly provided under 357 | this License. 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If your 375 | rights have been terminated and not permanently reinstated, you do not qualify to 376 | receive new licenses for the same material under section 10. 377 | 378 | ### 9. Acceptance Not Required for Having Copies. 379 | 380 | You are not required to accept this License in order to receive or run a copy of the 381 | Program. Ancillary propagation of a covered work occurring solely as a consequence of 382 | using peer-to-peer transmission to receive a copy likewise does not require 383 | acceptance. However, nothing other than this License grants you permission to 384 | propagate or modify any covered work. These actions infringe copyright if you do not 385 | accept this License. Therefore, by modifying or propagating a covered work, you 386 | indicate your acceptance of this License to do so. 387 | 388 | ### 10. Automatic Licensing of Downstream Recipients. 389 | 390 | Each time you convey a covered work, the recipient automatically receives a license 391 | from the original licensors, to run, modify and propagate that work, subject to this 392 | License. You are not responsible for enforcing compliance by third parties with this 393 | License. 394 | 395 | An “entity transaction” is a transaction transferring control of an 396 | organization, or substantially all assets of one, or subdividing an organization, or 397 | merging organizations. If propagation of a covered work results from an entity 398 | transaction, each party to that transaction who receives a copy of the work also 399 | receives whatever licenses to the work the party's predecessor in interest had or 400 | could give under the previous paragraph, plus a right to possession of the 401 | Corresponding Source of the work from the predecessor in interest, if the predecessor 402 | has it or can get it with reasonable efforts. 403 | 404 | You may not impose any further restrictions on the exercise of the rights granted or 405 | affirmed under this License. For example, you may not impose a license fee, royalty, 406 | or other charge for exercise of rights granted under this License, and you may not 407 | initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging 408 | that any patent claim is infringed by making, using, selling, offering for sale, or 409 | importing the Program or any portion of it. 410 | 411 | ### 11. Patents. 412 | 413 | A “contributor” is a copyright holder who authorizes use under this 414 | License of the Program or a work on which the Program is based. The work thus 415 | licensed is called the contributor's “contributor version”. 416 | 417 | A contributor's “essential patent claims” are all patent claims owned or 418 | controlled by the contributor, whether already acquired or hereafter acquired, that 419 | would be infringed by some manner, permitted by this License, of making, using, or 420 | selling its contributor version, but do not include claims that would be infringed 421 | only as a consequence of further modification of the contributor version. For 422 | purposes of this definition, “control” includes the right to grant patent 423 | sublicenses in a manner consistent with the requirements of this License. 424 | 425 | Each contributor grants you a non-exclusive, worldwide, royalty-free patent license 426 | under the contributor's essential patent claims, to make, use, sell, offer for sale, 427 | import and otherwise run, modify and propagate the contents of its contributor 428 | version. 429 | 430 | In the following three paragraphs, a “patent license” is any express 431 | agreement or commitment, however denominated, not to enforce a patent (such as an 432 | express permission to practice a patent or covenant not to sue for patent 433 | infringement). To “grant” such a patent license to a party means to make 434 | such an agreement or commitment not to enforce a patent against the party. 435 | 436 | If you convey a covered work, knowingly relying on a patent license, and the 437 | Corresponding Source of the work is not available for anyone to copy, free of charge 438 | and under the terms of this License, through a publicly available network server or 439 | other readily accessible means, then you must either (1) cause the Corresponding 440 | Source to be so available, or (2) arrange to deprive yourself of the benefit of the 441 | patent license for this particular work, or (3) arrange, in a manner consistent with 442 | the requirements of this License, to extend the patent license to downstream 443 | recipients. “Knowingly relying” means you have actual knowledge that, but 444 | for the patent license, your conveying the covered work in a country, or your 445 | recipient's use of the covered work in a country, would infringe one or more 446 | identifiable patents in that country that you have reason to believe are valid. 447 | 448 | If, pursuant to or in connection with a single transaction or arrangement, you 449 | convey, or propagate by procuring conveyance of, a covered work, and grant a patent 450 | license to some of the parties receiving the covered work authorizing them to use, 451 | propagate, modify or convey a specific copy of the covered work, then the patent 452 | license you grant is automatically extended to all recipients of the covered work and 453 | works based on it. 454 | 455 | A patent license is “discriminatory” if it does not include within the 456 | scope of its coverage, prohibits the exercise of, or is conditioned on the 457 | non-exercise of one or more of the rights that are specifically granted under this 458 | License. You may not convey a covered work if you are a party to an arrangement with 459 | a third party that is in the business of distributing software, under which you make 460 | payment to the third party based on the extent of your activity of conveying the 461 | work, and under which the third party grants, to any of the parties who would receive 462 | the covered work from you, a discriminatory patent license (a) in connection with 463 | copies of the covered work conveyed by you (or copies made from those copies), or (b) 464 | primarily for and in connection with specific products or compilations that contain 465 | the covered work, unless you entered into that arrangement, or that patent license 466 | was granted, prior to 28 March 2007. 467 | 468 | Nothing in this License shall be construed as excluding or limiting any implied 469 | license or other defenses to infringement that may otherwise be available to you 470 | under applicable patent law. 471 | 472 | ### 12. No Surrender of Others' Freedom. 473 | 474 | If conditions are imposed on you (whether by court order, agreement or otherwise) 475 | that contradict the conditions of this License, they do not excuse you from the 476 | conditions of this License. If you cannot convey a covered work so as to satisfy 477 | simultaneously your obligations under this License and any other pertinent 478 | obligations, then as a consequence you may not convey it at all. For example, if you 479 | agree to terms that obligate you to collect a royalty for further conveying from 480 | those to whom you convey the Program, the only way you could satisfy both those terms 481 | and this License would be to refrain entirely from conveying the Program. 482 | 483 | ### 13. Use with the GNU Affero General Public License. 484 | 485 | Notwithstanding any other provision of this License, you have permission to link or 486 | combine any covered work with a work licensed under version 3 of the GNU Affero 487 | General Public License into a single combined work, and to convey the resulting work. 488 | The terms of this License will continue to apply to the part which is the covered 489 | work, but the special requirements of the GNU Affero General Public License, section 490 | 13, concerning interaction through a network will apply to the combination as such. 491 | 492 | ### 14. Revised Versions of this License. 493 | 494 | The Free Software Foundation may publish revised and/or new versions of the GNU 495 | General Public License from time to time. Such new versions will be similar in spirit 496 | to the present version, but may differ in detail to address new problems or concerns. 497 | 498 | Each version is given a distinguishing version number. If the Program specifies that 499 | a certain numbered version of the GNU General Public License “or any later 500 | version” applies to it, you have the option of following the terms and 501 | conditions either of that numbered version or of any later version published by the 502 | Free Software Foundation. If the Program does not specify a version number of the GNU 503 | General Public License, you may choose any version ever published by the Free 504 | Software Foundation. 505 | 506 | If the Program specifies that a proxy can decide which future versions of the GNU 507 | General Public License can be used, that proxy's public statement of acceptance of a 508 | version permanently authorizes you to choose that version for the Program. 509 | 510 | Later license versions may give you additional or different permissions. However, no 511 | additional obligations are imposed on any author or copyright holder as a result of 512 | your choosing to follow a later version. 513 | 514 | ### 15. Disclaimer of Warranty. 515 | 516 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. 517 | EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 518 | PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER 519 | EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 520 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE 521 | QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE 522 | DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 523 | 524 | ### 16. Limitation of Liability. 525 | 526 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY 527 | COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS 528 | PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, 529 | INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE 530 | PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE 531 | OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE 532 | WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 533 | POSSIBILITY OF SUCH DAMAGES. 534 | 535 | ### 17. Interpretation of Sections 15 and 16. 536 | 537 | If the disclaimer of warranty and limitation of liability provided above cannot be 538 | given local legal effect according to their terms, reviewing courts shall apply local 539 | law that most closely approximates an absolute waiver of all civil liability in 540 | connection with the Program, unless a warranty or assumption of liability accompanies 541 | a copy of the Program in return for a fee. 542 | 543 | END OF TERMS AND CONDITIONS 544 | 545 | ## How to Apply These Terms to Your New Programs 546 | 547 | If you develop a new program, and you want it to be of the greatest possible use to 548 | the public, the best way to achieve this is to make it free software which everyone 549 | can redistribute and change under these terms. 550 | 551 | To do so, attach the following notices to the program. It is safest to attach them 552 | to the start of each source file to most effectively state the exclusion of warranty; 553 | and each file should have at least the “copyright” line and a pointer to 554 | where the full notice is found. 555 | 556 | 557 | Copyright (C) 558 | 559 | This program is free software: you can redistribute it and/or modify 560 | it under the terms of the GNU General Public License as published by 561 | the Free Software Foundation, either version 3 of the License, or 562 | (at your option) any later version. 563 | 564 | This program is distributed in the hope that it will be useful, 565 | but WITHOUT ANY WARRANTY; without even the implied warranty of 566 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 567 | GNU General Public License for more details. 568 | 569 | You should have received a copy of the GNU General Public License 570 | along with this program. If not, see . 571 | 572 | Also add information on how to contact you by electronic and paper mail. 573 | 574 | If the program does terminal interaction, make it output a short notice like this 575 | when it starts in an interactive mode: 576 | 577 | Copyright (C) 578 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 579 | This is free software, and you are welcome to redistribute it 580 | under certain conditions; type `show c' for details. 581 | 582 | The hypothetical commands `show w' and `show c' should show the appropriate parts of 583 | the General Public License. Of course, your program's commands might be different; 584 | for a GUI interface, you would use an “about box”. 585 | 586 | You should also get your employer (if you work as a programmer) or school, if any, to 587 | sign a “copyright disclaimer” for the program, if necessary. For more 588 | information on this, and how to apply and follow the GNU GPL, see 589 | <>. 590 | 591 | The GNU General Public License does not permit incorporating your program into 592 | proprietary programs. If your program is a subroutine library, you may consider it 593 | more useful to permit linking proprietary applications with the library. If this is 594 | what you want to do, use the GNU Lesser General Public License instead of this 595 | License. But first, please read 596 | <>. 597 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """ 2 | kgrid: reciprocal-space sampling for ab-initio materials chemistry 3 | """ 4 | 5 | from os.path import abspath, dirname 6 | from setuptools import setup, find_packages 7 | 8 | project_dir = abspath(dirname(__file__)) 9 | 10 | setup( 11 | name='kgrid', 12 | version='1.2.0', 13 | description='Reciprocal space sampling for atomistic crystal structures', 14 | long_description=""" 15 | Generate reciprocal-space grids with scalar cutoff parameters and standard 16 | crystal structure files. kgrid helps with k-point convergence problems when 17 | using ab initio codes that lack a single-parameter option, and help you 18 | understand and plan calculations with codes that do. 19 | """, 20 | long_description_content_type='text/markdown', 21 | url='https://github.com/WMD-group/kgrid', 22 | author='Adam J. Jackson', 23 | author_email='a.j.jackson@physics.org', 24 | license='GPL v3', 25 | classifiers=[ 26 | 'Development Status :: 3 - Alpha', 27 | 'Intended Audience :: Science/Research', 28 | 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 29 | 'Natural Language :: English', 30 | 'Programming Language :: Python :: 3.6', 31 | 'Topic :: Scientific/Engineering :: Chemistry', 32 | 'Topic :: Scientific/Engineering :: Physics' 33 | ], 34 | keywords='chemistry physics k-point sampling reciprocal', 35 | packages=find_packages(exclude=['test']), 36 | python_requires='>=3.6, <4', 37 | install_requires=['ase>=3.18'], 38 | entry_points={ 39 | 'console_scripts': [ 40 | 'kgrid = kgrid.cli:main', 41 | 'kgrid-series = kgrid.series:main' 42 | ] 43 | } 44 | ) 45 | -------------------------------------------------------------------------------- /test/data/POSCAR: -------------------------------------------------------------------------------- 1 | SiO2 2 | 1.00000000000000 3 | 4.2266540199664249 0.0000000000000000 0.0000000000000000 4 | 0.0000000000000000 4.2266540199664249 0.0000000000000000 5 | 0.0000000000000000 0.0000000000000000 2.6888359272289208 6 | Si O 7 | 2 4 8 | Direct 9 | 0.0000000000000000 0.0000000000000000 0.0000000000000000 10 | 0.5000000000000000 0.5000000000000000 0.5000000000000000 11 | 0.3067891334429594 0.3067891334429594 0.0000000000000000 12 | 0.6932108665570406 0.6932108665570406 0.0000000000000000 13 | 0.1932108665570406 0.8067891334429594 0.5000000000000000 14 | 0.8067891334429594 0.1932108665570406 0.5000000000000000 15 | -------------------------------------------------------------------------------- /test/data/geometry.in: -------------------------------------------------------------------------------- 1 | # Ga2O3 2 | 3 | lattice_vector 12.2139997482 0.0000000000 0.0000000000 4 | lattice_vector 0.0000000000 3.0369999409 0.0000000000 5 | lattice_vector -1.3859651379 0.0000000000 5.6299114558 6 | 7 | 8 | atom_frac 0.090499997 0.000000000 0.794600010 Ga 9 | atom_frac 0.909500003 0.000000000 0.205399990 Ga 10 | atom_frac 0.590499997 0.500000000 0.794600010 Ga 11 | atom_frac 0.409500003 0.500000000 0.205399990 Ga 12 | atom_frac 0.158659995 0.500000000 0.314020008 Ga 13 | atom_frac 0.841340005 0.500000000 0.685979962 Ga 14 | atom_frac 0.658659995 0.000000000 0.314020008 Ga 15 | atom_frac 0.341340005 0.000000000 0.685979962 Ga 16 | atom_frac 0.164499998 0.000000000 0.109800003 O 17 | atom_frac 0.835500002 0.000000000 0.890200019 O 18 | atom_frac 0.664499998 0.500000000 0.109800003 O 19 | atom_frac 0.335500002 0.500000000 0.890200019 O 20 | atom_frac 0.173299998 0.000000000 0.563199997 O 21 | atom_frac 0.826699972 0.000000000 0.436800003 O 22 | atom_frac 0.673300028 0.500000000 0.563199997 O 23 | atom_frac 0.326700002 0.500000000 0.436800003 O 24 | atom_frac 0.995899975 0.500000000 0.256599993 O 25 | atom_frac 0.004100025 0.500000000 0.743399978 O 26 | atom_frac 0.495899916 0.000000000 0.256599993 O 27 | atom_frac 0.504100025 0.000000000 0.743399978 O 28 | -------------------------------------------------------------------------------- /test/test_kgrid_cli.py: -------------------------------------------------------------------------------- 1 | import pathlib 2 | 3 | import pytest 4 | 5 | import kgrid.cli 6 | 7 | data_dir = pathlib.Path('test/data') 8 | sio2 = data_dir / 'POSCAR' 9 | 10 | 11 | def test_calc_grid_output(capsys): 12 | kgrid.cli.calc_grid(15., filename=str(sio2), pretty_print=True) 13 | captured = capsys.readouterr() 14 | 15 | assert captured.out == ' 8 8 12\n' 16 | 17 | 18 | def test_calc_grid_format(tmp_path): 19 | tmpdir = tmp_path / "calc-grid" 20 | tmpdir.mkdir() 21 | 22 | with open(sio2) as fd: 23 | poscar_data = fd.read() 24 | 25 | (tmpdir / 'ambiguous-name').write_text(poscar_data) 26 | 27 | assert kgrid.cli.calc_grid(15., filename=(tmpdir / 'ambiguous-name'), 28 | filetype='vasp') == (8, 8, 12) 29 | 30 | 31 | @pytest.mark.parametrize('args, expected_args, expected_kwargs', 32 | [(['the_file', '-a', '12'], 33 | [12], {'filename': 'the_file', 34 | 'mode': 'vasp_auto', 35 | 'filetype': False, 36 | 'realspace': False, 37 | 'pretty_print': True}), 38 | (['the_cell_file', '--castep_spacing', '0.05', 39 | '-t', 'castep'], 40 | [0.05], {'filename': 'the_cell_file', 41 | 'mode': 'castep_mp_spacing', 42 | 'filetype': 'castep', 43 | 'realspace': False, 44 | 'pretty_print': True}), 45 | (['the_file', '-r'], 46 | [10], {'filename': 'the_file', 47 | 'mode': 'default', 48 | 'filetype': False, 49 | 'realspace': True, 50 | 'pretty_print': True}), 51 | ]) 52 | def test_kgrid_main(mocker, args, expected_args, expected_kwargs): 53 | mocked_calc_grid = mocker.patch('kgrid.cli.calc_grid', 54 | return_value=None) 55 | 56 | kgrid.cli.main(params=args) 57 | 58 | mocked_calc_grid.assert_called_with(*expected_args, **expected_kwargs) 59 | -------------------------------------------------------------------------------- /test/test_kgrid_lib.py: -------------------------------------------------------------------------------- 1 | import pathlib 2 | 3 | import pytest 4 | import ase.io 5 | 6 | import kgrid 7 | 8 | data_dir = pathlib.Path('test/data') 9 | sio2 = ase.io.read(data_dir / 'POSCAR') 10 | ga2o3 = ase.io.read(data_dir / 'geometry.in') 11 | 12 | 13 | @pytest.mark.parametrize('atoms, expected, kwargs', 14 | [(sio2, (5, 5, 8), {}), 15 | (ga2o3, (2, 7, 4), {}), 16 | (sio2, (2, 2, 4), {'mode': 'vasp_auto'}), 17 | (sio2, (5, 5, 8), {'mode': 'kspacing', 18 | 'cutoff_length': 0.3}), 19 | (sio2, (5, 5, 8), {'mode': 'castep_mp_spacing', 20 | 'cutoff_length': 0.05})]) 21 | def test_calc_kpt_tuple(atoms, expected, kwargs): 22 | assert kgrid.calc_kpt_tuple(atoms, **kwargs) == expected 23 | -------------------------------------------------------------------------------- /test/test_kgrid_series_cli.py: -------------------------------------------------------------------------------- 1 | import pathlib 2 | 3 | from numpy.testing import assert_almost_equal 4 | import ase 5 | import ase.io 6 | import pytest 7 | 8 | import kgrid.series 9 | 10 | data_dir = pathlib.Path('test/data') 11 | sio2_file = data_dir / 'POSCAR' 12 | sio2_atoms = ase.io.read(sio2_file) 13 | 14 | nearly_cubic_atoms = ase.Atoms('Ag', cell=[1.0, 1.01, 1.001]) 15 | 16 | def test_get_increments(): 17 | assert kgrid.series.get_increments([1, 2, 5]) == (0.5, 0.25, 0.1) 18 | 19 | 20 | @pytest.mark.parametrize('args, kwargs, expected', 21 | [([sio2_atoms, 3., 9.], {}, 22 | [4.0333, 4.2267, 5.3777, 6.34, 23 | 6.7221, 8.0665, 8.4533]), 24 | ([nearly_cubic_atoms, 20, 21], {}, 25 | [20., 20.02, 20.2, 20.5, 20.5205, 20.705]), 26 | ([nearly_cubic_atoms, 20, 21], {'decimals': 1}, 27 | [20., 20.2, 20.5, 20.7]) 28 | ]) 29 | def test_cutoff_series(args, kwargs, expected): 30 | result = kgrid.series.cutoff_series(*args, **kwargs) 31 | assert_almost_equal(result, expected) 32 | 33 | 34 | @pytest.mark.parametrize('params, expected', 35 | [([str(sio2_file), '-t', 'vasp', 36 | '--min=4', '--max', '7', 37 | '--comma_sep'], 38 | "2 2 3,2 2 4,3 3 4,3 3 5,4 4 5\n"), 39 | ([str(sio2_file), 40 | '--min=2', '--max', '4', 41 | '--castep'], 42 | ('Length cutoff MP SPACING Samples\n' 43 | '------------- ---------- ------------\n' 44 | ' 2.113 0.236597 1 1 2\n' 45 | ' 2.689 0.185957 2 2 2\n' 46 | )),]) 47 | def test_cli_output(capsys, params, expected): 48 | kgrid.series.main(params) 49 | captured = capsys.readouterr() 50 | 51 | assert captured.out == expected 52 | --------------------------------------------------------------------------------