├── .github └── workflows │ ├── pylint.yml │ └── pytest.yml ├── .gitignore ├── CHANGELOG.md ├── README.md ├── license.md ├── mctools ├── __init__.py ├── generic │ ├── __init__.py │ ├── fold_prim.py │ ├── get_energy.py │ ├── get_minimum.py │ ├── get_primitive.py │ ├── get_spacegroup.py │ ├── get_volume.py │ └── vectors.py ├── mace │ ├── __init__.py │ └── tail_mace_fit.py ├── other │ ├── __init__.py │ ├── plot_cplap_ternary.py │ ├── sendto.py │ └── sqs_read.py ├── phonon │ ├── __init__.py │ └── phonon_dispersion_compare.py └── vasp │ ├── __init__.py │ ├── get_vbm.py │ └── vasp_charge.py ├── pyproject.toml └── tests ├── test_get_energy.py ├── test_get_primitive.py └── test_get_spacegroup.py /.github/workflows/pylint.yml: -------------------------------------------------------------------------------- 1 | name: Pylint 2 | 3 | on: [push] 4 | 5 | jobs: 6 | build: 7 | runs-on: ubuntu-latest 8 | strategy: 9 | matrix: 10 | python-version: ["3.11"] 11 | steps: 12 | - uses: actions/checkout@v3 13 | - name: Set up Python ${{ matrix.python-version }} 14 | uses: actions/setup-python@v3 15 | with: 16 | python-version: ${{ matrix.python-version }} 17 | - name: Install dependencies 18 | run: | 19 | python -m pip install --upgrade pip 20 | pip install pylint 21 | pip install . 22 | - name: Analysing the code with pylint 23 | run: | 24 | pylint $(git ls-files 'mctools/*.py') --fail-under 8.1 25 | -------------------------------------------------------------------------------- /.github/workflows/pytest.yml: -------------------------------------------------------------------------------- 1 | name: Pytest 2 | 3 | on: [push] 4 | 5 | jobs: 6 | build: 7 | runs-on: ubuntu-latest 8 | strategy: 9 | matrix: 10 | python-version: ["3.9", "3.11"] 11 | steps: 12 | - uses: actions/checkout@v3 13 | - name: Set up Python ${{ matrix.python-version }} 14 | uses: actions/setup-python@v3 15 | with: 16 | python-version: ${{ matrix.python-version }} 17 | - name: Install dependencies 18 | run: | 19 | python -m pip install --upgrade pip 20 | python -m pip install pytest flake8 flake8-pytest-style 21 | pip install . 22 | - name: Lint the test files with flake8-pytest-style 23 | run: | 24 | flake8 tests/ 25 | - name: Test with pytest 26 | run: | 27 | pytest 28 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | mctools.egg-info -------------------------------------------------------------------------------- /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 | ### Packaging and testing 18 | - mctools now uses a pyproject.toml file 19 | - the mctools package has been reorganised into submodules, grouping tools that have a similar scope 20 | - mctools now includes a few tests; automatic testing and linting are run with github actions 21 | 22 | ### Compatibility 23 | - `get_spacegroup` and `get_primitive` are made compatible with modern versions of spglib 24 | 25 | ### Major changes 26 | - get_primitive output format has changed and is now a lot more legible 27 | - output format can be controlled with `--precision` argument 28 | 29 | - `ase-convert` has been removed: use `ase convert` instead 30 | 31 | ### New tools 32 | - multi-phonon-dispersion plotter based on Euphonic 33 | - live MACE fitting plotter 34 | 35 | ## [1.1] - 2024-04-19 36 | Slap a version number on "unreleased" stuff before API-breaking v2 37 | 38 | - "sendto" now looks for a config file in home directory 39 | - "sendto" options to skip large VASP files 40 | - New CPLAP plotter 41 | - Add "get-minimum" for quick extraction of low-energy structure from trajectory 42 | 43 | ## [1.0] - 2017-04-25 44 | 45 | - Add "get-volume" for quick read of volume 46 | - Add "get-energy" for quick read of energy 47 | - Update all "get" tools for Python3 compatibility and simpler interface 48 | - Input file is now consistently the first positional argument so no 49 | need to remember which optional flag is needed. 50 | 51 | ## [0.2] - 2016-03-01 52 | 53 | - Fix broken get-spacegroup interface 54 | - Add reader/converter for ATAT SQS files 55 | 56 | ## 0.1 - 2016-11-04 57 | 58 | - Begin proper organisation of repository and packaging 59 | - Tools collected from various projects 60 | - Reasonably functional components 61 | - ase-convert 62 | - get-primitive 63 | - get-spacegroup 64 | - vectors 65 | - Primitive / work-in-progress 66 | - get-vbm 67 | - vasp-charge 68 | - Possibly too "personal" 69 | - sendto 70 | - Packaging with pip 71 | - GPL license 72 | 73 | [Unreleased]: https://github.com/ajjackson/mctools/compare/v1.1...HEAD 74 | [1.1]: https://github.com/ajjackson/mctools/compare/v1.0...v1.1 75 | [1.0]: https://github.com/ajjackson/mctools/compare/v0.2...v1.0 76 | [0.2]: https://github.com/ajjackson/mctools/compare/v0.1...v0.2 77 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # MCTOOLS 2 | 3 | Collection of generic pre- and post- processing tools using the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase). 4 | Developed while working with [Walsh Materials Design](https://github.com/wmd-group), kept on as a personal toolkit 5 | and developed further while at [Scanlon Materials Theory Group](https://github.com/smtg-ucl). 6 | 7 | The recommended way of installing is to clone the repository and make a local installation using pip: 8 | 9 | ```bash 10 | git clone https://github.com/ajjackson/mctools.git 11 | cd mctools 12 | pip install --user -e . 13 | ``` 14 | 15 | To run unit tests, install pytest and run with 16 | ```bash 17 | python -m pytest 18 | ``` 19 | 20 | get-spacegroup (Spacegroup tolerances) 21 | -------------------------------------- 22 | Use [Spglib](http://spg.sourceforge.net) to analyse the symmetry of a 23 | crystal structure file over a range of distance thresholds. This can 24 | be useful for identifying when numerical noise or limited convergence 25 | has resulted in a lower-symmetry spacegroup, as well as for quickly 26 | checking the identity of an unknown structure. Call with `-h` flag for 27 | usage information. 28 | 29 | ``` 30 | # EXAMPLE 31 | bash> get_spacegroup.py -i geometry.in.next_step 32 | | Threshold / Å | Space group | 33 | |---------------|-------------------| 34 | | 0.00001 | P-1 (2) | 35 | | 0.00010 | P-1 (2) | 36 | | 0.00050 | C2/m (12) | 37 | | 0.00100 | C2/m (12) | 38 | | 0.00500 | P-3m1 (164) | 39 | | 0.01000 | P-3m1 (164) | 40 | | 0.05000 | P-3m1 (164) | 41 | | 0.10000 | P-3m1 (164) | 42 | ``` 43 | 44 | get-minimum (Extract optimum from trajectory) 45 | --------------------------------------------- 46 | Use ASE to import a trajectory, typically a vasprun.xml or OUTCAR file 47 | from a structure relaxation. Find the step with lowest energy and 48 | write it out to a file. This is useful for salvaging optimisation 49 | calculations that get 'lost'. 50 | 51 | get-primitive (Primitive cell generator) 52 | ---------------------------------------- 53 | Use [Spglib](http://spg.sourceforge.net) to generate a primitive cell 54 | from/to any ASE-supported structure file format. It can be helpful to 55 | use **get_spacegroup.py** first in order to identify an appropriate 56 | symmetry threshold. Call with `-h` flag for usage information. 57 | 58 | plot-cplap-ternary (Pretty plotting for CPLAP outputs) 59 | ------------------------------------------------------ 60 | This is an alternative plotter to the GNUplot scripts generated by the 61 | Chemical Potential Limits Analysis Program (CPLAP). 62 | ([website](https://sourceforge.net/projects/cplap/), 63 | [paper](https://doi.org/10.1016/j.cpc.2013.08.026)) 64 | Specifically it deals with analysis of ternary systems where one phase is set 65 | as the dependent variable. 66 | All of the necessary data is read from the *grid.dat* and 67 | *2Dplot.txt* output files, including the elements and compound 68 | formulae. The chemical potential of the dependent element is 69 | displayed as a colour map on the stability region. 70 | The plotter makes use of various matplotlib features (choice of file 71 | formats, appearance customisation with style sheets) to generate 72 | publication/presentation-quality graphics. 73 | 74 | sendto (submission to remote server) 75 | ------------------------------------ 76 | 77 | Copy the current directory to a specified remote server. The server 78 | accounts must be set up in sendto.conf. This is a convenience tool for 79 | copying files around, and does not submit to a queue. 80 | 81 | sqs-read (ATAT SQS file reader) 82 | ------------------------------- 83 | 84 | Read a "bestsqs.out" file as generated by the 85 | [ATAT mcsqs](https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/manual/node46.html) 86 | tool. Print to standard output, optionally write 87 | file or open ASE GUI. 88 | 89 | fold-prim (ATAT/BANDUP glue) 90 | ---------------------------- 91 | 92 | Computing the unfolded band structure of a disordered or alloy 93 | material requires a reference primitive cell, but it makes no 94 | sense to compute such a cell. This tool will generate a "dummy" 95 | primitive cell from a relaxed supercell, given the supercell 96 | matrix. 97 | 98 | 99 | vasp-charge (Electron counting) 100 | ------------------------------- 101 | 102 | WORK IN PROGRESS 103 | 104 | Report the number of electrons in a proposed vasp calculation 105 | (NELECT). The name refers to an intended feature (specify system 106 | charge). At the moment there is no real user interface. 107 | 108 | Uses the VASP_PP_PATH environment variable; if you use ASE for VASP 109 | calculations this should be set up. Otherwise it will not work. 110 | 111 | vectors (Lattice vectors) 112 | ------------------------- 113 | 114 | Report lattice vectors in a, b, c, alpha, beta, gamma format. This is 115 | useful for comparing structures and makes for more compact and 116 | intuitive reporting. Call with `-h` flag for usage information. 117 | 118 | ``` 119 | # EXAMPLE 120 | bash> vectors.py geometry.in 121 | a b c alpha beta gamma 122 | 11.451 3.856 6.193 90.00 103.21 90.00 123 | ``` 124 | 125 | Related Repositories 126 | ------ 127 | ###### [k-grid (Mesh densities)](https://github.com/WMD-Bath/kgrid) 128 | Optimal k-point meshes with a single convergence parameter 129 | ###### [RVO (Optimisation tool)](https://github.com/WMD-Bath/rvo) 130 | Rapid volume optimisation with an auxiliary equation of state 131 | -------------------------------------------------------------------------------- /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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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 | -------------------------------------------------------------------------------- /mctools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajjackson/mctools/21b331d144e884bf0a5e91cb21232310f664607f/mctools/__init__.py -------------------------------------------------------------------------------- /mctools/generic/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajjackson/mctools/21b331d144e884bf0a5e91cb21232310f664607f/mctools/generic/__init__.py -------------------------------------------------------------------------------- /mctools/generic/fold_prim.py: -------------------------------------------------------------------------------- 1 | """Get primitive cell from supercell""" 2 | from argparse import ArgumentParser 3 | from os.path import isfile 4 | from json import loads 5 | from ase import Atoms 6 | import ase.io 7 | from numpy import matrix 8 | from numpy.linalg import inv 9 | 10 | 11 | def fold_prim(supercell_file, supercell_matrix, output='prim_cell_lattice.in'): 12 | """Get a primitive cell corresponding to a supercell 13 | 14 | Args: 15 | supercell_file (str): Path to supercell structure file. This should be 16 | a format recognised by ASE. 17 | supercell_matrix (str): Supercell expansion of the primitive cell. This 18 | is a 3x3 matrix, which can be expressed as a string with the format 19 | "[[ax, ay, az], [bx, by, bz], [cx, cy, cz]]" or without punctuation 20 | as "ax ay az bx by bz cx cy cz" or a path to an atat str file in 21 | which case lines 4-6 will be read in as a 3x3 matrix. 22 | output (str): Filename for output of dummy structure with correct 23 | lattice vectors. If None, do not write file. 24 | 25 | Returns: 26 | ase.Atoms: 27 | dummy structure with correct lattice vectors 28 | """ 29 | 30 | r_supercell = matrix(ase.io.read(supercell_file).cell) 31 | 32 | if isfile(supercell_matrix): 33 | with open(supercell_matrix, 'r', encoding="utf-8") as f: 34 | for i in range(3): 35 | f.readline() 36 | rows = [f.readline() for i in range(3)] 37 | 38 | supercell_matrix = [[float(x) for x in row.split()] for row in rows] 39 | supercell_matrix = matrix(supercell_matrix) 40 | print(supercell_matrix) 41 | 42 | elif '[' in supercell_matrix: 43 | supercell_matrix = matrix(loads(supercell_matrix)) 44 | 45 | else: 46 | supercell_matrix = [float(x) for x in supercell_matrix.split()] 47 | assert len(supercell_matrix) == 9 48 | supercell_matrix = matrix(supercell_matrix) 49 | supercell_matrix = supercell_matrix.reshape((3, 3)) 50 | 51 | new_cell = inv(supercell_matrix) * r_supercell 52 | 53 | atoms = Atoms('X', cell=new_cell) 54 | 55 | if output is not None: 56 | ase.io.write(output, atoms, format='vasp', vasp5=True) 57 | 58 | return atoms 59 | 60 | 61 | def main(): # pylint: disable=missing-function-docstring 62 | parser = ArgumentParser(description=""" 63 | Get a dummy primitive cell, given a supercell structure and matrix. 64 | The purpose of this is to set up calculations with BANDUP, which may 65 | require a primitive cell for a disordered phase. The given supercell 66 | matrix is inverted to obtain appropriate lattice vectors for the 67 | development of a k-point path. 68 | """) 69 | 70 | parser.add_argument('file', type=str, 71 | help="Structure file for relaxed supercell") 72 | parser.add_argument( 73 | 'matrix', type=str, 74 | help="""Supercell matrix. Either provide a path to an ATAT structure 75 | file, or provide matrix as a quoted string in form 76 | '[[ax, ay, az], [bx, by, bz], [cx, cy, cz]]' 77 | or 'ax ay az bx by bz cx cy cz' """) 78 | parser.add_argument('-o', '--output', type=str, 79 | default='prim_cell_lattice.in', 80 | help="Path for output file in VASP format.") 81 | 82 | args = parser.parse_args() 83 | 84 | fold_prim(supercell_file=args.file, 85 | supercell_matrix=args.matrix, 86 | output=args.output) 87 | -------------------------------------------------------------------------------- /mctools/generic/get_energy.py: -------------------------------------------------------------------------------- 1 | from argparse import ArgumentParser 2 | from typing import List, Optional 3 | 4 | import ase.io 5 | 6 | 7 | def get_energy(filename): 8 | """Wrap ASE to get calculated energy from output file""" 9 | atoms = ase.io.read(filename) 10 | return atoms.get_total_energy() 11 | 12 | 13 | def main(params: Optional[List[str]] = None): 14 | """Get calculated energy from output file using ASE""" 15 | 16 | parser = ArgumentParser(description="Read energy from output") 17 | parser.add_argument("filename", type=str, nargs='?', 18 | default="vasprun.xml", 19 | help="Path to ab initio output file") 20 | 21 | if params: 22 | args = parser.parse_args(params) 23 | else: 24 | args = parser.parse_args() 25 | 26 | energy = get_energy(args.filename) 27 | print(energy) 28 | 29 | 30 | if __name__ == '__main__': 31 | main() 32 | -------------------------------------------------------------------------------- /mctools/generic/get_minimum.py: -------------------------------------------------------------------------------- 1 | import argparse 2 | import ase.io 3 | 4 | 5 | def main(): 6 | parser = argparse.ArgumentParser( 7 | description="Get the minimum-energy structure from a trajectory") 8 | parser.add_argument( 9 | 'input_file', 10 | type=str, 11 | default='POSCAR', 12 | help="Path to crystal structure file, recognisable by ASE") 13 | parser.add_argument( 14 | '--input_format', 15 | type=str, 16 | help="Format for input file (needed if ASE can't guess from filename)") 17 | parser.add_argument( 18 | '-o', '--output_file', default='POSCAR.min', 19 | help="Path/filename for output") 20 | parser.add_argument( 21 | '--output_format', 22 | type=str, 23 | help="Format for input file (needed if ASE can't guess from filename)") 24 | args = parser.parse_args() 25 | get_minimum(**vars(args)) 26 | 27 | 28 | def get_minimum(input_file='POSCAR', 29 | input_format=None, 30 | output_file=None, 31 | output_format=None): 32 | try: 33 | if input_format is None: 34 | traj = ase.io.read(input_file, index=':') 35 | else: 36 | traj = ase.io.read(input_file, index=':', format=input_format) 37 | except IOError as e: 38 | raise Exception("I/O error({0}): {1}".format(e.errno, e.strerror)) 39 | 40 | atoms = min(traj, key=(lambda a: a.get_total_energy())) 41 | 42 | if output_format is None: 43 | try: 44 | atoms.write(output_file, vasp5=True, direct=True) 45 | except TypeError: 46 | atoms.write(output_file) 47 | elif output_format == "vasp": 48 | atoms.write(output_file, format="vasp", vasp5=True, direct=True) 49 | else: 50 | atoms.write(output_file, format=output_format) 51 | -------------------------------------------------------------------------------- /mctools/generic/get_primitive.py: -------------------------------------------------------------------------------- 1 | """Get primitive cell from crystal structure using spglib""" 2 | 3 | from argparse import ArgumentParser 4 | from pathlib import Path 5 | from typing import Any, Dict, List, Optional 6 | 7 | import ase 8 | import ase.io 9 | import spglib 10 | 11 | 12 | def get_parser() -> ArgumentParser: 13 | parser = ArgumentParser( 14 | description="Find a primitive unit cell using spglib") 15 | parser.add_argument( 16 | "input_file", 17 | type=Path, 18 | default="POSCAR", 19 | help="Path to crystal structure file, recognisable by ASE", 20 | ) 21 | parser.add_argument( 22 | "--input-format", 23 | dest="input_format", 24 | type=str, 25 | help="Format for input file (needed if ASE can't guess from filename)", 26 | ) 27 | parser.add_argument( 28 | "-t", 29 | "--threshold", 30 | type=float, 31 | default=1e-05, 32 | help=( 33 | "Distance threshold in AA for symmetry reduction " 34 | "(corresponds to spglib 'symprec' keyword)" 35 | ), 36 | ) 37 | parser.add_argument( 38 | "-a", 39 | "--angle-tolerance", 40 | dest="angle_tolerance", 41 | type=float, 42 | default=-1.0, 43 | help="Angle tolerance for symmetry reduction", 44 | ) 45 | parser.add_argument( 46 | "-o", 47 | "--output-file", 48 | type=Path, 49 | default=None, 50 | dest="output_file", 51 | help="Path/filename for output", 52 | ) 53 | parser.add_argument( 54 | "--output-format", 55 | dest="output_format", 56 | type=str, 57 | default=None, 58 | help="Format for input file (needed if ASE can't guess from filename)", 59 | ) 60 | parser.add_argument( 61 | "-v", 62 | "--verbose", 63 | action="store_true", 64 | help="Print output to screen even when writing to file.", 65 | ) 66 | parser.add_argument( 67 | "-p", 68 | "--precision", 69 | type=int, 70 | help=("Number of decimal places for float display. " 71 | "(Output files are not affected)"), 72 | default=6, 73 | ) 74 | return parser 75 | 76 | 77 | def main(params: Optional[List[str]] = None): 78 | parser = get_parser() 79 | 80 | if params: 81 | args = parser.parse_args(params) 82 | else: 83 | args = parser.parse_args() 84 | 85 | get_primitive(**snake_case_args(vars(args))) 86 | 87 | 88 | def snake_case_args(kwarg_dict: Dict[str, Any]) -> Dict[str, Any]: 89 | """Convert user-friendly hyphenated arguments to python_friendly ones""" 90 | return {key.replace("-", "_"): value for key, value in kwarg_dict.items()} 91 | 92 | 93 | def get_primitive_atoms( 94 | atoms: ase.Atoms, 95 | threshold: float = 1e-5, 96 | angle_tolerance: float = -1.0, 97 | print_spacegroup: bool = False, 98 | ) -> ase.Atoms: 99 | """Convert ASE Atoms to primitive cell using spglib""" 100 | atoms_spglib = ( 101 | atoms.cell.array, 102 | atoms.get_scaled_positions(), 103 | atoms.numbers, 104 | ) 105 | 106 | spacegroup = spglib.get_spacegroup( 107 | atoms_spglib, symprec=threshold, angle_tolerance=angle_tolerance) 108 | if print_spacegroup: 109 | print(f"Space group: {spacegroup}") 110 | 111 | cell, positions, atomic_numbers = spglib.find_primitive( 112 | atoms_spglib, symprec=threshold, angle_tolerance=angle_tolerance) 113 | 114 | primitive_atoms = ase.Atoms( 115 | scaled_positions=positions, 116 | cell=cell, 117 | numbers=atomic_numbers, 118 | pbc=True) 119 | 120 | return primitive_atoms 121 | 122 | 123 | def get_primitive(input_file: Path = Path('POSCAR'), 124 | input_format: Optional[str] = None, 125 | output_file: Optional[Path] = None, 126 | output_format: Optional[str] = None, 127 | threshold: float = 1e-5, 128 | angle_tolerance: float = -1., 129 | verbose: bool = False, 130 | precision: int = 6) -> None: 131 | 132 | if output_file is None: 133 | verbose = True 134 | 135 | float_format_str = f"{{:{precision+4}.{precision}f}}" 136 | 137 | def format_float(x: float) -> str: 138 | return float_format_str.format(x) 139 | 140 | atoms = ase.io.read(input_file, format=input_format) 141 | atoms = get_primitive_atoms( 142 | atoms, threshold=threshold, angle_tolerance=angle_tolerance, print_spacegroup=verbose 143 | ) 144 | 145 | if verbose: 146 | print("Primitive cell vectors:") 147 | for row in atoms.cell: 148 | print(" ".join(map(format_float, row))) 149 | 150 | print("Atomic positions and proton numbers:") 151 | for position, number in zip(atoms.get_scaled_positions(), atoms.numbers): 152 | print(" ".join(map(format_float, position)) + f"\t{number}") 153 | 154 | if output_file is None: 155 | pass 156 | else: 157 | 158 | atoms.write(output_file, format=output_format) 159 | -------------------------------------------------------------------------------- /mctools/generic/get_spacegroup.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | import argparse 4 | from pathlib import Path 5 | from typing import Optional 6 | 7 | import ase.io 8 | import spglib 9 | 10 | 11 | def get_default_file() -> Path: 12 | for candidate in ("geometry.in", "POSCAR", "castep.cell"): 13 | if (structure_file := Path.cwd() / candidate).is_file(): 14 | return structure_file 15 | 16 | raise ValueError("Input file not specified, no default found.") 17 | 18 | 19 | def get_spacegroup(filename: Optional[Path] = None, 20 | filetype: Optional[str] = None): 21 | 22 | if filename is None: 23 | filename = get_default_file() 24 | 25 | atoms = ase.io.read(str(filename), format=filetype) 26 | cell = (atoms.cell.array, atoms.get_scaled_positions(), atoms.numbers) 27 | 28 | print("| Threshold / Å | Space group |") 29 | print("|---------------|-------------------|") 30 | 31 | for threshold in (1e-5, 1e-4, 5e-4, 1e-3, 5e-3, 1e-2, 5e-2, 1e-1): 32 | print("| {0:0.5f} | {1: <16} |".format( 33 | threshold, spglib.get_spacegroup(cell, symprec=threshold))) 34 | 35 | 36 | def main(): 37 | parser = argparse.ArgumentParser() 38 | parser.add_argument("filename", type=Path, default=None, nargs="?", 39 | help="Input structure file") 40 | parser.add_argument("-f", "--filetype", type=str, default=None, 41 | help="File format for ASE importer") 42 | args = parser.parse_args() 43 | get_spacegroup(filename=args.filename, filetype=args.filetype) 44 | -------------------------------------------------------------------------------- /mctools/generic/get_volume.py: -------------------------------------------------------------------------------- 1 | ############################################################################### 2 | # Copyright 2017 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 ase.io 19 | from argparse import ArgumentParser 20 | 21 | 22 | def get_volume(filename): 23 | atoms = ase.io.read(filename) 24 | return atoms.get_volume() 25 | 26 | 27 | def main(): 28 | parser = ArgumentParser(description="Read volume from chemical structure") 29 | parser.add_argument("filename", type=str, nargs='?', 30 | default="geometry.in", 31 | help="Path to input file [default: ./geometry.in]") 32 | 33 | args = parser.parse_args() 34 | 35 | volume = get_volume(args.filename) 36 | print(volume) 37 | -------------------------------------------------------------------------------- /mctools/generic/vectors.py: -------------------------------------------------------------------------------- 1 | # -*- encoding: utf-8 -*- 2 | """Get lattice vector in a, b, c, α, β, γ format from ase-compatible file""" 3 | 4 | ############################################################################### 5 | # Copyright 2015 Adam Jackson 6 | ############################################################################### 7 | # This program is free software: you can redistribute it and/or modify 8 | # it under the terms of the GNU General Public License as published by 9 | # the Free Software Foundation, either version 3 of the License, or 10 | # (at your option) any later version. 11 | # 12 | # This program is distributed in the hope that it will be useful, 13 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 14 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 15 | # GNU General Public License for more details. 16 | # 17 | # You should have received a copy of the GNU General Public License 18 | # along with this program. If not, see . 19 | ############################################################################### 20 | 21 | from optparse import OptionParser 22 | import numpy as np 23 | import ase.io 24 | 25 | 26 | def main(): 27 | 28 | parser = OptionParser() 29 | parser.add_option("-f", "--file", 30 | action="store", type="string", dest="input_file", 31 | default="geometry.in", 32 | help="Path to input file [default: ./geometry.in]") 33 | parser.add_option("-l", "--latex", 34 | action="store_true", dest="latex_format", default=False, 35 | help="""Print in convenient format for insertion in latex 36 | tabular environments""") 37 | parser.add_option("-p", "--precision", "--precision_length", 38 | action="store", type="int", dest="precision_length", 39 | default=3, help="""Number of decimal places to return 40 | (length in Angstroms)""") 41 | parser.add_option("-a", "--precision_angle", 42 | action="store", type="int", dest="precision_angle", 43 | default=2, help="""Number of decimal places to return 44 | (angle in degrees)""") 45 | # Add further options here 46 | (options, args) = parser.parse_args() 47 | 48 | # Read file and extract lattice vectors 49 | atoms = ase.io.read(options.input_file) 50 | lattice_matrix = np.array(atoms.get_cell()) 51 | 52 | # Get lattice vector magnitudes (a, b, c) according to Pythagoras' theorem 53 | (a, b, c) = np.sqrt(np.sum(np.square(lattice_matrix), 1)) 54 | 55 | # Calculate angles between vectors using relation 56 | # A.B = |A||B|cos(theta) 57 | gamma = np.arccos(lattice_matrix[0, :].dot(lattice_matrix[1, :]) 58 | / (np.linalg.norm(lattice_matrix[0, :]) 59 | * np.linalg.norm(lattice_matrix[1, :]))) 60 | 61 | alpha = np.arccos(lattice_matrix[1, :].dot(lattice_matrix[2, :]) 62 | / (np.linalg.norm(lattice_matrix[1, :]) 63 | * np.linalg.norm(lattice_matrix[2, :]))) 64 | 65 | beta = np.arccos(lattice_matrix[2, :].dot(lattice_matrix[0, :]) 66 | / (np.linalg.norm(lattice_matrix[2, :]) 67 | * np.linalg.norm(lattice_matrix[0, :]))) 68 | 69 | # Convert to degrees 70 | (alpha, beta, gamma) = np.array([alpha, beta, gamma]).dot(180/np.pi) 71 | 72 | if options.latex_format: 73 | print('{0:6.{6}f}&{1:6.{6}f}&{2:6.{6}f}&{3:6.{7}f}&' 74 | '{4:6.{7}f}&{5:6.{7}f}'.format(a, b, c, alpha, beta, gamma, 75 | options.precision_length, 76 | options.precision_angle)) 77 | else: 78 | print(' a {0}b {0}c {0}alpha{1}beta{1} gamma'.format( 79 | options.precision_length*" ", options.precision_angle*" ")) 80 | print('{0:.{6}f} {1:.{6}f} {2:.{6}f} {3:.{7}f} {4:.{7}f} ' 81 | '{5:.{7}f}'.format(a, b, c, alpha, beta, gamma, 82 | options.precision_length, 83 | options.precision_angle)) 84 | -------------------------------------------------------------------------------- /mctools/mace/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajjackson/mctools/21b331d144e884bf0a5e91cb21232310f664607f/mctools/mace/__init__.py -------------------------------------------------------------------------------- /mctools/mace/tail_mace_fit.py: -------------------------------------------------------------------------------- 1 | """Realtime visualisation of fitting progress for MACE potential""" 2 | from argparse import ArgumentParser 3 | import os 4 | from pathlib import Path 5 | import re 6 | import subprocess 7 | 8 | import asciichartpy 9 | 10 | 11 | FLOAT = r"-?\d+\.\d+" 12 | EPOCH_RE = (rf".*Epoch (\d+): loss=({FLOAT}), " 13 | rf"RMSE_E_per_atom=({FLOAT}) meV, RMSE_F=({FLOAT}) meV / A.*") 14 | PLOT_CFG = {'height': 10, 'colors': [asciichartpy.blue]} 15 | 16 | 17 | def main(): 18 | """Realtime visualisation of fitting progress for MACE potential""" 19 | parser = ArgumentParser() 20 | parser.add_argument("logfile", type=Path, help="Path to MACE training log") 21 | parser.add_argument("--buffer", type=int, default=100, help="Max steps to show") 22 | args = parser.parse_args() 23 | 24 | 25 | epoch_re = re.compile(EPOCH_RE) 26 | 27 | epochs, losses, energies, forces = [], [], [], [] 28 | 29 | with subprocess.Popen(['tail', '-n', str(args.buffer), '-F', args.logfile], 30 | stdout=subprocess.PIPE, 31 | stderr=subprocess.PIPE) as tail_process: 32 | for line in tail_process.stdout: 33 | if (match := epoch_re.match(line.decode())): 34 | epoch, loss, energy, force = match.groups() 35 | 36 | epochs.append(int(epoch)) 37 | losses.append(float(loss)) 38 | energies.append(float(energy)) 39 | forces.append(float(force)) 40 | 41 | os.system("clear") 42 | epoch_slice = epochs[-args.buffer:] 43 | print(f"Epochs {epoch_slice[0]}-{epoch_slice[-1]}") 44 | 45 | for title, data in [(f"Loss {losses[-1]}", losses), 46 | (f"Energy/atom RMSE (meV) {energies[-1]}", energies), 47 | (f"Force RMSE (meV / A) {forces[-1]}", forces)]: 48 | 49 | print(f"\n{title}") 50 | print(asciichartpy.plot(data[-args.buffer:], PLOT_CFG)) 51 | 52 | else: 53 | pass 54 | -------------------------------------------------------------------------------- /mctools/other/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajjackson/mctools/21b331d144e884bf0a5e91cb21232310f664607f/mctools/other/__init__.py -------------------------------------------------------------------------------- /mctools/other/plot_cplap_ternary.py: -------------------------------------------------------------------------------- 1 | from argparse import ArgumentParser 2 | import re 3 | from collections import OrderedDict 4 | from math import ceil 5 | import numpy as np 6 | from scipy.spatial import ConvexHull 7 | import matplotlib 8 | import matplotlib.pyplot as plt 9 | from matplotlib.patches import Polygon 10 | from matplotlib.gridspec import GridSpec 11 | 12 | 13 | def main(): 14 | parser = ArgumentParser( 15 | description="Plot a ternary system from CPLAP outputs") 16 | parser.add_argument('-o', '--output', type=str, default=None, 17 | help='Output plot filename. Default: plot to screen') 18 | parser.add_argument('-g', '--grid-file', type=str, default='grid.dat', 19 | dest='grid_file', 20 | help='Path to grid.dat file from CPLAP') 21 | parser.add_argument('-t', '--txt-file', type=str, default='2Dplot.txt', 22 | dest='txt_file', 23 | help='Path to 2Dplot.txt file from CPLAP') 24 | parser.add_argument('--xmin', type=float, default=None, 25 | help='x-axis lower limit') 26 | parser.add_argument('--ymin', type=float, default=None, 27 | help='y-axis lower limit') 28 | parser.add_argument('--style', type=str, nargs='+', default=['ggplot'], 29 | help=('Path to Matplotlib style file(s) and/or name(s)' 30 | ' of inbuilt styles.')) 31 | parser.add_argument('--cmap', type=str, default='viridis', 32 | help=('Matplotlib colormap')) 33 | parser.add_argument('--width', type=float, default=6) 34 | parser.add_argument('--height', type=float, default=4) 35 | parser.add_argument('--ratio', type=int, nargs='+', default=[4], 36 | help=('Fraction of width occupied by plot vs colorbar:' 37 | ' give one or two integers. E.g. --ratio 4 gives' 38 | ' 4:1 ratio, --ratio 7 3 gives 7:3 ratio. ' 39 | 'You may need to tune this when using --width.')) 40 | group = parser.add_mutually_exclusive_group() 41 | group.add_argument('--gridlines', action='store_true', 42 | dest='gridlines', default=None) 43 | group.add_argument('--no-gridlines', action='store_false', 44 | dest='gridlines') 45 | args = parser.parse_args() 46 | plot_cplap_ternary(**vars(args)) 47 | 48 | 49 | def plot_cplap_ternary(output='plot-2d.pdf', 50 | grid_file='grid.dat', txt_file='2Dplot.txt', 51 | xmin=None, ymin=None, 52 | style=['ggplot'], cmap='viridis', 53 | width=6, height=4, ratio=[4], 54 | gridlines=None): 55 | # Set Truetype PDF/PS fonts unless overruled by style file 56 | matplotlib.rcParams['pdf.fonttype'] = 42 57 | matplotlib.rcParams['ps.fonttype'] = 42 58 | if len(style) > 0: 59 | matplotlib.style.use(style) 60 | 61 | fig = plt.figure(figsize=(width, height)) 62 | 63 | if len(ratio) == 1: 64 | ratio += [1] 65 | elif len(ratio) > 2: 66 | raise ValueError('Ratio can be given as one or two integers. ' 67 | '{} is too many!'.format(len(ratio))) 68 | gs = GridSpec(1, ratio[0] + ratio[1]) 69 | ax = fig.add_subplot(gs.new_subplotspec((0, ratio[1]), colspan=ratio[0])) 70 | cax = fig.add_subplot(gs.new_subplotspec((0, 0), colspan=ratio[1])) 71 | 72 | with open(grid_file, 'rt') as f: 73 | 74 | # Scroll to formula and read 75 | for _ in range(3): 76 | line = f.readline() 77 | el_matches = re.findall(r'\d+ (\w+)', line) 78 | 79 | # Scroll to number of points and read 80 | for _ in range(4): 81 | line = f.readline() 82 | npts = 5 83 | npts_matches = re.findall(r'first\s+(\d+) points', line) 84 | 85 | if len(npts_matches) == 1: 86 | npts = int(npts_matches[0]) 87 | else: 88 | raise Exception("Couldn't read number of polyhedron corners") 89 | 90 | # Scroll to data lines and read coordinates from npts lines 91 | for _ in range(5): 92 | f.readline() 93 | region = np.zeros((npts, 2)) 94 | 95 | for i in range(npts): 96 | line = f.readline().split() 97 | x, y = float(line[0]), float(line[1]) 98 | region[i, :] = x, y 99 | 100 | # # Use convex hull solver to draw polyhedron edges in correct order 101 | # hull = np.array([region[i] for i in ConvexHull(region).vertices]) 102 | # region_patch = Polygon(hull, facecolor=(0.6, 0.6, 0.6)) 103 | # ax.add_patch(region_patch) 104 | 105 | # Read in rest of mesh, skipping header, region and '|' column 106 | mesh = np.genfromtxt('grid.dat', skip_header=(12 + npts), 107 | usecols=(0, 1, 3)) 108 | mesh_x = sorted(set(mesh[:, 0])) 109 | mesh_y = sorted(set(mesh[:, 1])) 110 | mesh_z = np.zeros((len(mesh_y), len(mesh_x))) * np.NaN 111 | for x, y, z in mesh: 112 | ix = mesh_x.index(x) 113 | iy = mesh_y.index(y) 114 | mesh_z[iy, ix] = z 115 | mesh_z = np.ma.masked_invalid(mesh_z) 116 | dep_mu = ax.pcolormesh(mesh_x, mesh_y, mesh_z, rasterized=True, cmap=cmap) 117 | cbar = fig.colorbar(dep_mu, cax=cax) 118 | cbar.set_label(r'$\mu$ ({}) / eV'.format(el_matches[2])) 119 | 120 | with open('2Dplot.txt', 'rt') as f: 121 | lines = f.readlines() 122 | 123 | data = OrderedDict() 124 | 125 | for i in range(len(lines) // 4 + 1): 126 | species = lines[i * 4][1:-1] 127 | 128 | x1, y1 = map(float, lines[i * 4 + 1].split()) 129 | x2, y2 = map(float, lines[i * 4 + 2].split()) 130 | 131 | data[species] = [[x1, x2], [y1, y2]] 132 | 133 | if xmin is None: 134 | xmin = ceil(min(min(coords[0]) for coords in data.values())) 135 | if ymin is None: 136 | ymin = ceil(min(min(coords[1]) for coords in data.values())) 137 | 138 | for species, (x, y) in data.items(): 139 | ax.plot(x, y, '-', label=format_chem(species)) 140 | 141 | ax.legend() 142 | ax.set_xlim(xmin, 0) 143 | ax.set_ylim(ymin, 0) 144 | ax.set_xlabel(r'$\mu$ ({}) / eV'.format(el_matches[0])) 145 | ax.xaxis.set_label_position('top') 146 | ax.xaxis.set_ticks_position('top') 147 | ax.set_ylabel(r'$\mu$ ({}) / eV'.format(el_matches[1])) 148 | ax.yaxis.set_label_position('right') 149 | ax.yaxis.set_ticks_position('right') 150 | 151 | # Gridlines option can overrule style defaults 152 | if gridlines is not None: 153 | ax.grid(gridlines) 154 | 155 | fig.tight_layout() 156 | 157 | if output is None: 158 | plt.show() 159 | else: 160 | fig.savefig(output) 161 | 162 | 163 | def format_chem(species): 164 | text = re.findall(r'\D+', species) 165 | nums = re.findall(r'\d+', species) 166 | chem = '' 167 | for t, n, in zip(text, nums): 168 | chem += t 169 | chem += r'$_{{{}}}$'.format(n) 170 | if len(text) > len(nums): 171 | chem += text[-1] 172 | return chem 173 | 174 | if __name__ == '__main__': 175 | main() 176 | -------------------------------------------------------------------------------- /mctools/other/sendto.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | import os 4 | from os.path import basename, dirname, abspath, join, isfile 5 | import argparse 6 | 7 | try: 8 | from configparser import ConfigParser 9 | except ImportError: 10 | from ConfigParser import ConfigParser 11 | 12 | import subprocess 13 | 14 | 15 | def sendto(server=False, project=False, folders=False, nw=False): 16 | 17 | if not server: 18 | raise Exception('No remote server defined') 19 | 20 | conf_file = join(os.environ['HOME'], '.sendto.conf') 21 | if not isfile(conf_file): 22 | raise Exception("No config file found. Server names should be " 23 | "set up with calculation directories " 24 | "in {0}".format(conf_file)) 25 | 26 | conf = ConfigParser() 27 | conf.read(conf_file) 28 | rundir = conf.get(server, 'rundir') 29 | 30 | # Use current directory if none provided 31 | if len(folders) == 0: 32 | folders = ['os.path.curdir'] 33 | 34 | for calc in folders: 35 | calc = abspath(calc) 36 | # If project isn't given use name of directory two levels 37 | # above (Assumes structure /parents/PROJECTS/runs/RUNDIRS) 38 | if not project: 39 | project = basename(dirname(dirname(calc))) 40 | 41 | rsync_call = ['rsync', '-avzu', calc, 42 | ':'.join((server, os.path.join(rundir, 43 | project)))] 44 | 45 | if nw: 46 | rsync_call += ['--exclude', 'WAVECAR', 47 | '--exclude', 'CHGCAR', 48 | '--exclude', 'CHG'] 49 | 50 | subprocess.call(rsync_call) 51 | 52 | 53 | def get_args(): 54 | parser = argparse.ArgumentParser( 55 | description="Send calculations folder(s) to remote server" 56 | ) 57 | parser.add_argument('server', type=str, 58 | help="Server name from SSH config") 59 | parser.add_argument('-p', '--project', type=str, default=False, 60 | help="Project ID (guess if not provided)") 61 | parser.add_argument('--nw', '--no-wavecar', action='store_true', 62 | help="Don't include wavecar, chgcar, chg") 63 | parser.add_argument('folders', type=str, nargs='*') 64 | args = parser.parse_args() 65 | return vars(args) 66 | 67 | 68 | def main(): 69 | args = get_args() 70 | sendto(**args) 71 | 72 | if __name__ == '__main__': 73 | main() 74 | -------------------------------------------------------------------------------- /mctools/other/sqs_read.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | from __future__ import print_function, absolute_import 3 | 4 | import argparse 5 | import numpy as np 6 | import ase.atoms 7 | import ase.build 8 | import ase.visualize 9 | 10 | def atoms_from_sqs(filename): 11 | 12 | with open(filename, 'r') as f: 13 | lines = f.readlines() 14 | lines = [line.split() for line in lines] 15 | 16 | basis = np.matrix([list(map(float, line)) for line in lines[:3]]) 17 | scell = np.matrix([list(map(float, line)) for line in lines[3:6]]) 18 | 19 | spositions = [np.matrix(list(map(float, line[:3]))) for line in lines[6:]] 20 | symbols = [line[-1] for line in lines[6:]] 21 | 22 | supercell = scell * basis 23 | positions = spositions * basis 24 | atoms = ase.atoms.Atoms(symbols=symbols, 25 | cell=supercell, 26 | positions=positions, 27 | pbc=True) 28 | 29 | return atoms 30 | 31 | def txt_display(atoms): 32 | print("Unit cell:") 33 | print(atoms.cell) 34 | print("Positions") 35 | atoms = ase.build.sort(atoms) 36 | for atom in atoms: 37 | 38 | print(atom.position, atom.symbol) 39 | 40 | def main(): 41 | parser = argparse.ArgumentParser() 42 | parser.add_argument('filename', nargs='?', default='bestsqs.out', 43 | help="Input file generated by ATAT") 44 | parser.add_argument('--output', '-o', default=None, 45 | help="If specified, write to this filename") 46 | parser.add_argument('--gui', '-g', action='store_true', 47 | help="Show structure in ASE-GUI") 48 | 49 | args = parser.parse_args() 50 | 51 | atoms = atoms_from_sqs(args.filename) 52 | 53 | if args.output is not None: 54 | # Write file with vasp5 flag if supported 55 | try: 56 | atoms.write(args.output, sort=True, vasp5=True) 57 | except TypeError: 58 | atoms = ase.build.sort(atoms) 59 | atoms.write(args.output) 60 | else: 61 | txt_display(atoms) 62 | 63 | if args.gui: 64 | ase.visualize.view(atoms) 65 | 66 | if __name__ == '__main__': 67 | main() 68 | -------------------------------------------------------------------------------- /mctools/phonon/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajjackson/mctools/21b331d144e884bf0a5e91cb21232310f664607f/mctools/phonon/__init__.py -------------------------------------------------------------------------------- /mctools/phonon/phonon_dispersion_compare.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from argparse import ArgumentParser 3 | from pathlib import Path 4 | from typing import List, Optional 5 | 6 | from euphonic import ForceConstants, ureg 7 | from euphonic.cli.utils import _bands_from_force_constants, load_data_from_file 8 | from euphonic.plot import plot_1d, plot_1d_to_axis 9 | from matplotlib import pyplot as plt 10 | from matplotlib.axes import Axes 11 | 12 | 13 | def get_parser() -> ArgumentParser: 14 | parser = ArgumentParser() 15 | parser.add_argument( 16 | "filenames", nargs="+", type=Path, help="Force constants data files" 17 | ) 18 | parser.add_argument( 19 | "--labels", 20 | nargs="+", 21 | type=str, 22 | default=None, 23 | help="Labels corresponding to filenames", 24 | ) 25 | parser.add_argument( 26 | "--save", 27 | type=Path, 28 | nargs='?', 29 | default=None, 30 | const="bands.pdf", 31 | help="Save figure to file", 32 | ) 33 | parser.add_argument( 34 | "--title", 35 | type=str, 36 | default=None, 37 | help="Figure title" 38 | ) 39 | parser.add_argument( 40 | "--legend-axis", 41 | dest="legend_axis", 42 | type=int, 43 | default=0, 44 | help=("Index for band segment with legend. " 45 | "(Use this when the first segment is short!)") 46 | ) 47 | return parser 48 | 49 | 50 | def plot_bands( 51 | fc: ForceConstants, axes: Optional[List[Axes]], color="C0" 52 | ) -> List[Axes]: 53 | bands, x_tick_labels, split_args = _bands_from_force_constants( 54 | fc, 55 | q_distance=(0.01 * ureg("1/angstrom")), 56 | asr="reciprocal", 57 | dipole=True, 58 | ) 59 | bands.reorder_frequencies() 60 | spectrum = bands.get_dispersion() 61 | spectrum.x_tick_labels = x_tick_labels 62 | 63 | if axes is None: 64 | # plot_1d creates a final invisible axis: the rest are 65 | # segments of the band structure. 66 | fig = plot_1d(spectrum.split(**split_args), color=color) 67 | axes = fig.axes[:-1] 68 | else: 69 | for ax, segment in zip(axes, spectrum.split(**split_args)): 70 | plot_1d_to_axis(segment, ax, color=color) 71 | 72 | return axes 73 | 74 | 75 | def main(): 76 | args = get_parser().parse_args() 77 | 78 | data = [load_data_from_file(filename) for filename in args.filenames] 79 | for fc, filename in zip(data, args.filenames): 80 | if not isinstance(fc, ForceConstants): 81 | print( 82 | "Cannot use {filename}, this script only " 83 | "works with force constants" 84 | ) 85 | sys.exit() 86 | 87 | axes = None 88 | for i, fc in enumerate(data): 89 | axes = plot_bands(fc, axes, color=f'C{i}') 90 | 91 | # There are a lot of lines, to get a sensible legend 92 | # we just label one per file 93 | nbands = int(len(axes[0].lines) / len(data)) 94 | labels = args.labels if args.labels else [str(f) for f in args.filenames] 95 | axes[args.legend_axis].legend(axes[0].lines[::nbands], labels) 96 | 97 | fig = axes[0].get_figure() 98 | if args.title: 99 | fig.suptitle(args.title) 100 | 101 | if args.save: 102 | fig.savefig(args.save) 103 | else: 104 | plt.show() 105 | -------------------------------------------------------------------------------- /mctools/vasp/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajjackson/mctools/21b331d144e884bf0a5e91cb21232310f664607f/mctools/vasp/__init__.py -------------------------------------------------------------------------------- /mctools/vasp/get_vbm.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import print_function, absolute_import 3 | 4 | try: 5 | from itertools import ifilter as filter 6 | except ImportError: 7 | pass 8 | 9 | import argparse 10 | try: 11 | import xml.etree.cElementTree as ET 12 | except ImportError: 13 | import xml.etree.ElementTree as ET 14 | 15 | def get_eigs(vasp_xml): 16 | """Read vasprun.xml file and get the eigenvalues 17 | 18 | Args: 19 | vasp_xml: path to "vasprun.xml" output file 20 | Returns: 21 | eig_sets: list of lists, grouped by k-point 22 | [[[kpt1_eig1 occ11], [kpt1_eig2, occ12]...] 23 | [[kpt2_eig1_occ21], [kpt2_eig2, occ22]...] ...] 24 | 25 | """ 26 | 27 | tree = ET.ElementTree(file=vasp_xml) 28 | 29 | # Get last set of eigenvalues 30 | eigs = list(tree.iter(tag='eigenvalues'))[-1] 31 | 32 | type(eigs) 33 | eig_sets = [eig_set.getchildren() 34 | for eig_set in eigs.iter('set') 35 | if ('comment' in eig_set.attrib 36 | and 'kpoint' in eig_set.attrib['comment'])] 37 | 38 | def eig_set_to_lists(eig_set): 39 | return list(map(lambda el: list(map(float, el.text.split())), eig_set)) 40 | 41 | eig_sets = list(map(eig_set_to_lists, eig_sets)) 42 | return eig_sets 43 | 44 | def get_max_eig_from_xml(vasp_xml): 45 | """ 46 | Read vasprun.xml and return highest occupied eigenvalue. 47 | 48 | If you included the right k-points this should be the VBM... 49 | """ 50 | eigs = get_eigs(vasp_xml) 51 | 52 | # Flatten from grouping by k-points with this nasty 53 | # double list comprehension 54 | 55 | all_eigs = [eig for kpt_eigs in eigs for eig in kpt_eigs] 56 | occupied = filter(lambda x: x[1] > 0., all_eigs) 57 | return max(x[0] for x in occupied) 58 | 59 | def main(): 60 | parser = argparse.ArgumentParser( 61 | description="Get the maximum occupied eigenvalue from a vasp run." 62 | ) 63 | parser.add_argument("xml_file", nargs='?', default='vasprun.xml', 64 | help="Path to vasprun.xml file") 65 | args = parser.parse_args() 66 | 67 | print(get_max_eig_from_xml(args.xml_file)) 68 | 69 | if __name__ == '__main__': 70 | main() 71 | -------------------------------------------------------------------------------- /mctools/vasp/vasp_charge.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | from __future__ import print_function, absolute_import, division 4 | import argparse 5 | import os 6 | from math import ceil 7 | import ase.io 8 | 9 | def get_neutral_electrons(atoms, pp='PBE', setups={}): 10 | """Get the number of valence electrons in a neutral structure 11 | 12 | A summary is printed to the standard output. 13 | 14 | Arguments: 15 | 16 | atoms (ase.Atoms): ASE Atoms object corresponding to VASP 17 | calculation 18 | 19 | pp (str): Specify the potpaw directory. The usual aliases (LDA, 20 | PBE, PW91) are available, or the full name 21 | (e.g. 'potpaw_PBE') can be used 22 | 23 | setups (dict): Special POTCAR identities specified per-species 24 | as a dict. e.g. {'O': '_pv'} 25 | 26 | 27 | 28 | """ 29 | zvals = get_zval_dict(atoms, setups=setups, pp=pp) 30 | 31 | # Sum over atoms 32 | nelect = sum([zvals[el] for el in atoms.get_chemical_symbols()]) 33 | 34 | return nelect 35 | 36 | 37 | def get_zval(potcar): 38 | """Read ZVAL from a POTCAR file""" 39 | 40 | with open(potcar, 'r') as f: 41 | for line in f: 42 | if 'ZVAL' in line: 43 | break 44 | else: 45 | raise Exception('No ZVAL found in file {0}'.format(potcar)) 46 | 47 | line = line.strip() 48 | zval = line.split()[5].strip() 49 | 50 | return float(zval) 51 | 52 | def get_zval_dict(atoms, setups={}, pp='PBE'): 53 | """Set up a dictionary of ZVALs (default electron count)""" 54 | 55 | pp_aliases = {'LDA': 'potpaw', 56 | 'PBE': 'potpaw_PBE', 57 | 'PW91': 'potpaw_GGA'} 58 | 59 | if pp in pp_aliases: 60 | pp = pp_aliases[pp] 61 | 62 | pp_dir = os.path.join(os.environ['VASP_PP_PATH'], pp) 63 | 64 | elements = set(atoms.get_chemical_symbols()) 65 | zvals = {} 66 | for element in elements: 67 | if element in setups: 68 | potcar_path = os.path.join(pp_dir, 69 | element + setups[element], 70 | 'POTCAR') 71 | else: 72 | potcar_path = os.path.join(pp_dir, element, 'POTCAR') 73 | zvals[element] = get_zval(potcar_path) 74 | return zvals 75 | 76 | 77 | def report(atoms, nelect, charge=0, setups={}, pp='PBE'): 78 | """Report stats from nelect, suggest numbers of bands""" 79 | nelect = nelect - charge 80 | zvals = get_zval_dict(atoms, setups=setups, pp=pp) 81 | 82 | formula_str = atoms.get_chemical_formula() 83 | print("Chemical formula: {0}".format(formula_str)) 84 | for el, z in zvals.items(): 85 | print("{0:3s}:{1:10.2f}".format(el, z)) 86 | 87 | nbands_nospin = int(ceil(nelect / 2)) 88 | print("") 89 | print("Total electrons: {0}".format(nelect)) 90 | print("") 91 | print("Occupied bands for non-spin-polarised " 92 | "calc:{0:4d}".format(nbands_nospin)) 93 | print("Suggested NBANDS for parallelism in:") 94 | for ppn in (8, 12, 16, 24): 95 | nbands = int(ceil((nbands_nospin + 4) / ppn) * ppn) 96 | print("{0:3}:{1:10}".format(ppn, nbands)) 97 | 98 | def main(): 99 | parser = argparse.ArgumentParser( 100 | description="Get the expected numbers of electrons and bands") 101 | parser.add_argument( 102 | 'input_file', 103 | type=str, 104 | default='POSCAR', 105 | help="Path to crystal structure file, recognisable by ASE") 106 | args = parser.parse_args() 107 | 108 | atoms = ase.io.read(args.input_file) 109 | nelect = get_neutral_electrons(atoms) 110 | 111 | report(atoms, nelect) 112 | 113 | if __name__ == '__main__': 114 | main() 115 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [project] 6 | name = "mctools" 7 | version = "1.1" 8 | authors = [ 9 | {name = "Adam J. Jackson", email = "a.j.jackson@physics.org"}, 10 | ] 11 | description = "Convenience tools for computational materials chemistry" 12 | keywords = ["chemistry", "ASE", "DFT"] 13 | license = {text = "GPL v3"} 14 | classifiers=[ 15 | "Development Status :: 4 - Beta", 16 | "Intended Audience :: Science/Research", 17 | "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", 18 | "Natural Language :: English", 19 | "Programming Language :: Python :: 3", 20 | "Topic :: Scientific/Engineering :: Chemistry", 21 | "Topic :: Scientific/Engineering :: Physics", 22 | ] 23 | requires-python = ">=3.9" 24 | dependencies = [ 25 | "asciichartpy", 26 | "ase", 27 | "euphonic", 28 | "spglib", 29 | "matplotlib", 30 | ] 31 | 32 | [project.urls] 33 | Repository = "https://github.com/ajjackson/mctools" 34 | 35 | [tool.setuptools.dynamic] 36 | readme = {file = ["README.md"]} 37 | 38 | [tool.black] 39 | line-length = 79 40 | 41 | [project.scripts] 42 | fold-prim = "mctools.generic.fold_prim:main" 43 | get-energy = "mctools.generic.get_energy:main" 44 | get-minimum = "mctools.generic.get_minimum:main" 45 | get-primitive = "mctools.generic.get_primitive:main" 46 | get-spacegroup = "mctools.generic.get_spacegroup:main" 47 | get-vbm = "mctools.vasp.get_vbm:main" 48 | get-volume = "mctools.generic.get_volume:main" 49 | phonon-dispersion-compare = "mctools.phonon.phonon_dispersion_compare:main" 50 | plot-cplap-ternary = "mctools.other.plot_cplap_ternary:main" 51 | sqs-read = "mctools.other.sqs_read:main" 52 | sendto = "mctools.other.sendto:main" 53 | tail-mace-fit = "mctools.mace.tail_mace_fit:main" 54 | vasp-charge = "mctools.vasp.vasp_charge:main" 55 | vectors = "mctools.generic.vectors:main" 56 | -------------------------------------------------------------------------------- /tests/test_get_energy.py: -------------------------------------------------------------------------------- 1 | import ase.build 2 | from ase.calculators.singlepoint import SinglePointCalculator 3 | import ase.io 4 | import pytest 5 | 6 | from mctools.generic.get_energy import get_energy, main 7 | 8 | 9 | ENERGY = 3.141 10 | FILENAME = "methane.extxyz" 11 | 12 | 13 | @pytest.fixture 14 | def methane_with_energy() -> ase.Atoms: 15 | atoms = ase.build.molecule("CH4") 16 | atoms.calc = SinglePointCalculator(atoms, energy=ENERGY) 17 | return atoms 18 | 19 | 20 | def test_get_energy(methane_with_energy, tmp_path) -> None: 21 | ase.io.write(tmp_path / FILENAME, methane_with_energy) 22 | 23 | assert get_energy(tmp_path / FILENAME) == pytest.approx(ENERGY) 24 | 25 | 26 | def test_main(methane_with_energy, tmp_path, capsys) -> None: 27 | ase.io.write(tmp_path / FILENAME, methane_with_energy) 28 | 29 | main([str(tmp_path / FILENAME)]) 30 | captured = capsys.readouterr() 31 | assert float(captured.out) == pytest.approx(ENERGY) 32 | -------------------------------------------------------------------------------- /tests/test_get_primitive.py: -------------------------------------------------------------------------------- 1 | import textwrap 2 | 3 | import ase 4 | import ase.build 5 | from numpy.random import RandomState 6 | import pytest 7 | 8 | from mctools.generic.get_primitive import main 9 | 10 | 11 | FILENAME = "rattled_cu.extxyz" 12 | OUTFILENAME = "POSCAR" 13 | REF_STDOUT = textwrap.dedent( 14 | """\ 15 | Space group: Fm-3m (225) 16 | Primitive cell vectors: 17 | 0.000 1.805 1.805 18 | 1.805 0.000 1.805 19 | 1.805 1.805 0.000 20 | Atomic positions and proton numbers: 21 | 0.500 0.500 0.500\t29 22 | """ 23 | ) 24 | REF_POSCAR = textwrap.dedent( 25 | """\ 26 | Cu 27 | 1.0000000000000000 28 | 0.0000000000000000 1.8050080045893520 1.8050080045893520 29 | 1.8050080045893520 0.0000000000000000 1.8050080045893520 30 | 1.8050080045893520 1.8050080045893520 0.0000000000000000 31 | Cu 32 | 1 33 | Cartesian 34 | 1.8050080045893520 1.8050080045893520 1.8050080045893520 35 | """ # noqa:W291 36 | ) 37 | 38 | 39 | @pytest.fixture 40 | def rattled_cu() -> ase.Atoms: 41 | rng = RandomState(seed=1) 42 | 43 | atoms = ase.build.bulk("Cu", cubic=True) * (2, 2, 2) 44 | atoms.rattle(stdev=1e-3, seed=1) 45 | atoms.set_cell(atoms.cell.array + 1e-4 * rng.rand(3, 3)) 46 | 47 | return atoms 48 | 49 | 50 | def test_get_primitive(rattled_cu, tmp_path, capsys) -> None: 51 | rattled_cu.write(tmp_path / FILENAME) 52 | 53 | main([str(tmp_path / FILENAME), 54 | "--input-format=extxyz", 55 | "--threshold=1e-2", 56 | "--angle-tolerance=1", 57 | "-o", 58 | str(tmp_path / OUTFILENAME), 59 | "-v", 60 | "--precision=3" 61 | ]) 62 | 63 | captured = capsys.readouterr() 64 | assert captured.out == REF_STDOUT 65 | 66 | with open(tmp_path / OUTFILENAME, "r") as fd: 67 | assert fd.read() == REF_POSCAR 68 | -------------------------------------------------------------------------------- /tests/test_get_spacegroup.py: -------------------------------------------------------------------------------- 1 | import textwrap 2 | 3 | import ase.build 4 | from numpy import logical_not 5 | from numpy.random import RandomState 6 | import pytest 7 | 8 | from mctools.generic.get_spacegroup import get_spacegroup 9 | 10 | 11 | FILENAME = "cu_rattled.extxyz" 12 | 13 | REF_TEXT = textwrap.dedent( 14 | """\ 15 | | Threshold / Å | Space group | 16 | |---------------|-------------------| 17 | | 0.00001 | P1 (1) | 18 | | 0.00010 | P1 (1) | 19 | | 0.00050 | Pm (6) | 20 | | 0.00100 | Pm (6) | 21 | | 0.00500 | Pmc2_1 (26) | 22 | | 0.01000 | Fm-3m (225) | 23 | | 0.05000 | Fm-3m (225) | 24 | | 0.10000 | Fm-3m (225) | 25 | """ 26 | ) 27 | 28 | 29 | @pytest.fixture(scope="module") 30 | def symmetry_broken_cu() -> ase.Atoms: 31 | atoms = ase.build.bulk("Cu", cubic=True) * (2, 2, 2) 32 | 33 | rng = RandomState(seed=1) 34 | 35 | # Break symmetry by up to 0.01 on a mirror plane 36 | xy_plane = atoms.positions[:, 2] == 0.0 37 | atoms.positions[xy_plane, :2] += 5e-3 - 1e-2 * rng.rand(xy_plane.sum(), 2) 38 | 39 | # Break symmetry by up to 0.0001 elsewhere 40 | off_plane = logical_not(xy_plane) 41 | atoms.positions[off_plane] += 5e-5 - 1e-4 * rng.rand(off_plane.sum(), 3) 42 | 43 | return atoms 44 | 45 | 46 | def test_get_spacegroup(symmetry_broken_cu, tmp_path, capsys) -> None: 47 | symmetry_broken_cu.write(tmp_path / FILENAME) 48 | get_spacegroup(filename=str(tmp_path / FILENAME)) 49 | captured = capsys.readouterr() 50 | 51 | assert captured.out == REF_TEXT 52 | --------------------------------------------------------------------------------