diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index 844f1c0..8ec2de1 100644 --- a/.github/workflows/pypi.yaml +++ b/.github/workflows/pypi.yaml @@ -52,7 +52,7 @@ jobs: environment: name: pypi # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status: - # url: https://pypi.org/p/YOURPROJECT + url: https://pypi.org/project/dfttoolkit/ steps: - name: Retrieve release distributions diff --git a/dfttoolkit/__init__.py b/dfttoolkit/__init__.py index e69de29..833fa3c 100644 --- a/dfttoolkit/__init__.py +++ b/dfttoolkit/__init__.py @@ -0,0 +1,38 @@ +# from .benchmarking import BenchmarkAims +# from .custom_ase import CustomAims +# from .friction import FrictionTensor +# from .geometry import AimsGeometry, VaspGeometry, XSFGeometry, XYZGeometry +# from .output import AimsOutput, ELSIOutput +# from .parameters import AimsControl +# from .trajectory import MDTrajectory +# from .utils import math_utils, units +# from .utils.file_utils import aims_bin_path_prompt, check_required_files +# from .utils.geometry_utils import read_xyz_animation +# from .utils.periodic_table import PeriodicTable +# from .utils.run_utils import no_repeat +# from .vibrations import AimsVibrations, VaspVibrations +# from .visualise import VisualiseAims + +# __all__ = [ +# "BenchmarkAims", +# "CustomAims", +# "FrictionTensor", +# "AimsGeometry", +# "VaspGeometry", +# "XSFGeometry", +# "XYZGeometry", +# "AimsOutput", +# "ELSIOutput", +# "AimsControl", +# "MDTrajectory", +# "math_utils", +# "units", +# "aims_bin_path_prompt", +# "check_required_files", +# "read_xyz_animation", +# "PeriodicTable", +# "no_repeat", +# "AimsVibrations", +# "VaspVibrations", +# "VisualiseAims", +# ] diff --git a/dfttoolkit/base_parser.py b/dfttoolkit/base_parser.py index 38332f6..336a3e4 100644 --- a/dfttoolkit/base_parser.py +++ b/dfttoolkit/base_parser.py @@ -27,7 +27,7 @@ def __init__(self, supported_files, **kwargs): # Check if the file path exists if not os.path.isfile(kwargs[kwarg]): - raise ValueError(f"{kwargs[kwarg]} does not exist.") + raise FileNotFoundError(f"{kwargs[kwarg]} does not exist.") # Store the file paths self.file_paths[kwarg] = kwargs[kwarg] diff --git a/dfttoolkit/output.py b/dfttoolkit/output.py index 1b49606..923a76e 100644 --- a/dfttoolkit/output.py +++ b/dfttoolkit/output.py @@ -1323,33 +1323,33 @@ def read_elsi_as_csc( # Get the column pointer end = 128 + self.n_basis * 8 - col_ptr = np.frombuffer(self.lines[128:end], dtype=np.int64) - col_ptr = np.append(col_ptr, self.n_non_zero + 1) - col_ptr -= 1 + col_i = np.frombuffer(self.lines[128:end], dtype=np.int64) + col_i = np.append(col_i, self.n_non_zero + 1) + col_i -= 1 # Get the row index start = end + self.n_non_zero * 4 - row_idx = np.array(np.frombuffer(self.lines[end:start], dtype=np.int32)) - row_idx -= 1 + row_i = np.array(np.frombuffer(self.lines[end:start], dtype=np.int32)) + row_i -= 1 if header[2] == 0: # real - nnz_val = np.frombuffer( + nnz = np.frombuffer( self.lines[start : start + self.n_non_zero * 8], dtype=np.float64, ) else: # complex - nnz_val = np.frombuffer( + nnz = np.frombuffer( self.lines[start : start + self.n_non_zero * 16], dtype=np.complex128, ) if csc_format: return sp.csc_matrix( - (nnz_val, row_idx, col_ptr), shape=(self.n_basis, self.n_basis) + (nnz, row_i, col_i), shape=(self.n_basis, self.n_basis) ) else: return sp.csc_matrix( - (nnz_val, row_idx, col_ptr), shape=(self.n_basis, self.n_basis) + (nnz, row_i, col_i), shape=(self.n_basis, self.n_basis) ).toarray() diff --git a/dfttoolkit/parameters.py b/dfttoolkit/parameters.py index 7e73993..f8d5a25 100644 --- a/dfttoolkit/parameters.py +++ b/dfttoolkit/parameters.py @@ -1,4 +1,4 @@ -from typing import List +from typing import List, Literal, Union import dfttoolkit.utils.file_utils as fu from dfttoolkit.base_parser import BaseParser @@ -75,7 +75,9 @@ def add_keywords(self, **kwargs: dict) -> None: # TODO finish this raise NotImplementedError - def remove_keywords(self, *args: str) -> None: + def remove_keywords( + self, *args: str, output: Literal["overwrite", "print", "return"] = "return" + ) -> Union[None, List[str]]: """ Remove keywords from the control.in file. @@ -83,6 +85,15 @@ def remove_keywords(self, *args: str) -> None: ---------- *args : str Keywords to be removed from the control.in file. + output : Literal["overwrite", "print", "return"], default="overwrite" + Overwrite the original file, print the modified file to STDOUT, or return + the modified file as a list of '\\n' separated strings. + + Returns + ------- + Union[None, List[str]] + If output is "return", the modified file is returned as a list of '\\n' + separated strings. """ for keyword in args: @@ -90,8 +101,16 @@ def remove_keywords(self, *args: str) -> None: if keyword in line: self.lines.pop(i) - with open(self.path, "w") as f: - f.writelines(self.lines) + match output: + case "overwrite": + with open(self.path, "w") as f: + f.writelines(self.lines) + + case "print": + print(*self.lines, sep="") + + case "return": + return self.lines def get_keywords(self) -> dict: """ diff --git a/dfttoolkit/utils/__init__.py b/dfttoolkit/utils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/dfttoolkit/utils/math_utils.py b/dfttoolkit/utils/math_utils.py index c8af90b..04a3061 100644 --- a/dfttoolkit/utils/math_utils.py +++ b/dfttoolkit/utils/math_utils.py @@ -1,5 +1,6 @@ -from typing import Union from copy import deepcopy +from typing import Union + import numpy as np import numpy.typing as npt import scipy @@ -405,7 +406,7 @@ def apply_hann_window(data): return windowed_data -def norm_matrix_by_dagonal(matrix: np.array) -> np.array: +def norm_matrix_by_dagonal(matrix: npt.NDArray) -> npt.NDArray: """ Norms a matrix such that the diagonal becomes 1. @@ -437,7 +438,7 @@ def norm_matrix_by_dagonal(matrix: np.array) -> np.array: return new_matrix -def mae(delta: np.ndarray) -> float: +def mae(delta: np.ndarray) -> np.floating: """ Calculated the mean absolute error from a list of value differnces. @@ -455,7 +456,7 @@ def mae(delta: np.ndarray) -> float: return np.mean(np.abs(delta)) -def rel_mae(delta: np.ndarray, target_val: np.ndarray) -> float: +def rel_mae(delta: np.ndarray, target_val: np.ndarray) -> np.floating: """ Calculated the relative mean absolute error from a list of value differnces, given the target values. diff --git a/dfttoolkit/utils/run_utils.py b/dfttoolkit/utils/run_utils.py index 9400aca..ef1be1f 100644 --- a/dfttoolkit/utils/run_utils.py +++ b/dfttoolkit/utils/run_utils.py @@ -31,14 +31,20 @@ def no_repeat( def _no_repeat(func): @wraps(func) def wrapper(*args, **kwargs): - if not os.path.isdir(calc_dir): - raise ValueError(f"{calc_dir} is not a directory.") + # Override calc_dir in decorator call if given in func + if "calc_dir" in kwargs: + check_dir = kwargs["calc_dir"] + else: + check_dir = calc_dir + + if not os.path.isdir(check_dir): + raise ValueError(f"{check_dir} is not a directory.") if force: return func(*args, **kwargs) - if not os.path.isfile(f"{calc_dir}/{output_file}"): + if not os.path.isfile(f"{check_dir}/{output_file}"): return func(*args, **kwargs) else: - print(f"aims.out already exists in {calc_dir}. Skipping calculation.") + print(f"aims.out already exists in {check_dir}. Skipping calculation.") return wrapper diff --git a/poetry.lock b/poetry.lock index f2b8838..55596ac 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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Run FHI-aims calculations using a custom binary if specified by --run-aims. + + If the calculation has already been run (ie. if the directory + `custom_bin_aims_calcs` exists), the calculations will not be run again, unless the + user specifies `change_bin` as an option to --run-aims. + """ + + # Check if the directory already exists + if os.path.isdir("custom_bin_aims_calcs") and run_aims != "change_bin": + return "custom_bin_aims_calcs" + elif run_aims is not False: + cwd = os.path.dirname(os.path.realpath(__file__)) + binary = aims_bin_path_prompt(run_aims, cwd) + subprocess.run(["bash", f"{cwd}/run_aims.sh", binary, str(run_aims)]) + yield "custom_bin_aims_calcs" + else: + yield "default_aims_calcs" + + +@pytest.fixture(scope="session") +def tmp_dir(tmp_path_factory): + """Temporary directory for all tests to write files to""" + + d = tmp_path_factory.mktemp("tmp") + yield d + + +@pytest.fixture(scope="session") +def ref_data(): + cwd = os.path.dirname(os.path.realpath(__file__)) + with open(f"{cwd}/test_references.yaml", "r") as references: + yield yaml.safe_load(references) + + +@pytest.fixture(scope="session") +def cwd(): + yield os.path.dirname(os.path.realpath(__file__)) + + +@pytest.fixture(scope="session") +def default_calc_dir(cwd): + yield f"{cwd}/fixtures/default_aims_calcs/1/" diff --git a/tests/fixtures/elsi_files/D_spin_01_kpt_000001.csc b/tests/fixtures/elsi_files/D_spin_01_kpt_000001.csc new file mode 100644 index 0000000..dc191f2 Binary files /dev/null and b/tests/fixtures/elsi_files/D_spin_01_kpt_000001.csc differ diff --git a/tests/fixtures/manipulated_aims_files/1/control.in b/tests/fixtures/manipulated_aims_files/1/control.in new file mode 100644 index 0000000..e6e1181 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/1/control.in @@ -0,0 +1,145 @@ +output_level full +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/fixtures/manipulated_aims_files/10/control.in b/tests/fixtures/manipulated_aims_files/10/control.in new file mode 100644 index 0000000..1c60dd8 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/10/control.in @@ -0,0 +1,88 @@ +hse_unit b +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/fixtures/manipulated_aims_files/2/control.in b/tests/fixtures/manipulated_aims_files/2/control.in new file mode 100644 index 0000000..12bd563 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/2/control.in @@ -0,0 +1,147 @@ +spin collinear +default_initial_moment 1 +output_level full +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/fixtures/manipulated_aims_files/3/control.in b/tests/fixtures/manipulated_aims_files/3/control.in new file mode 100644 index 0000000..7d015f1 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/3/control.in @@ -0,0 +1,148 @@ +spin collinear +default_initial_moment 1 +include_spin_orbit non_self_consistent +output_level full +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/fixtures/manipulated_aims_files/4/control.in b/tests/fixtures/manipulated_aims_files/4/control.in new file mode 100644 index 0000000..d00339a --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/4/control.in @@ -0,0 +1,87 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/fixtures/manipulated_aims_files/5/control.in b/tests/fixtures/manipulated_aims_files/5/control.in new file mode 100644 index 0000000..286b7b1 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/5/control.in @@ -0,0 +1,144 @@ +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/fixtures/manipulated_aims_files/6/control.in b/tests/fixtures/manipulated_aims_files/6/control.in new file mode 100644 index 0000000..330436c --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/6/control.in @@ -0,0 +1,88 @@ +relax_unit_cell full +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/fixtures/manipulated_aims_files/7/control.in b/tests/fixtures/manipulated_aims_files/7/control.in new file mode 100644 index 0000000..fe0b9f0 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/7/control.in @@ -0,0 +1,148 @@ +sc_accuracy_rho 1e-10 +sc_accuracy_eev 1e-6 +sc_accuracy_etot 1e-12 +sc_accuracy_forces 1e-8 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/fixtures/manipulated_aims_files/8/control.in b/tests/fixtures/manipulated_aims_files/8/control.in new file mode 100644 index 0000000..287e2e9 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/8/control.in @@ -0,0 +1,92 @@ +sc_iter_limit 10 +sc_accuracy_rho 1e-10 +sc_accuracy_eev 1e-6 +sc_accuracy_etot 1e-12 +sc_accuracy_forces 1e-8 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for Si atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +# 2020/09/08 Added f function to "light" after reinspection of Delta test outcomes. +# This was done for all of Al-Cl and is a tricky decision since it makes +# "light" calculations measurably more expensive for these elements. +# Nevertheless, outcomes for P, S, Cl (and to some extent, Si) appear +# to justify this choice. +# +################################################################################ + species Si +# global species definitions + nucleus 14 + mass 28.0855 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 42 5.0 + radial_multiplier 1 + angular_grids specified + division 0.5866 50 + division 0.9616 110 + division 1.2249 194 + division 1.3795 302 +# division 1.4810 434 +# division 1.5529 590 +# division 1.6284 770 +# division 1.7077 974 +# division 2.4068 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 3 s 2. + valence 3 p 2. +# ion occupancy + ion_occ 3 s 1. + ion_occ 3 p 1. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.75 A, 2.0 A, 2.25 A, 2.75 A, 3.75 A +# +################################################################################ +# "First tier" - improvements: -571.96 meV to -37.03 meV + hydro 3 d 4.2 + hydro 2 p 1.4 + hydro 4 f 6.2 + ionic 3 s auto +# "Second tier" - improvements: -16.76 meV to -3.03 meV +# hydro 3 d 9 +# hydro 5 g 9.4 +# hydro 4 p 4 +# hydro 1 s 0.65 +# "Third tier" - improvements: -3.89 meV to -0.60 meV +# ionic 3 d auto +# hydro 3 s 2.6 +# hydro 4 f 8.4 +# hydro 3 d 3.4 +# hydro 3 p 7.8 +# "Fourth tier" - improvements: -0.33 meV to -0.11 meV +# hydro 2 p 1.6 +# hydro 5 g 10.8 +# hydro 5 f 11.2 +# hydro 3 d 1 +# hydro 4 s 4.5 +# Further basis functions that fell out of the optimization - noise +# level... < -0.08 meV +# hydro 4 d 6.6 +# hydro 5 g 16.4 +# hydro 4 d 9 diff --git a/tests/fixtures/manipulated_aims_files/9/control.in b/tests/fixtures/manipulated_aims_files/9/control.in new file mode 100644 index 0000000..3dd43b6 --- /dev/null +++ b/tests/fixtures/manipulated_aims_files/9/control.in @@ -0,0 +1,145 @@ +hse_unit b +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for O atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species O +# global species definitions + nucleus 8 + mass 15.9994 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 36 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2659 50 + division 0.4451 110 + division 0.6052 194 + division 0.7543 302 +# division 0.8014 434 +# division 0.8507 590 +# division 0.8762 770 +# division 0.9023 974 +# division 1.2339 1202 +# outer_grid 974 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 2 s 2. + valence 2 p 4. +# ion occupancy + ion_occ 2 s 1. + ion_occ 2 p 3. +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Constructed for dimers: 1.0 A, 1.208 A, 1.5 A, 2.0 A, 3.0 A +# +################################################################################ +# "First tier" - improvements: -699.05 meV to -159.38 meV + hydro 2 p 1.8 + hydro 3 d 7.6 + hydro 3 s 6.4 +# "Second tier" - improvements: -49.91 meV to -5.39 meV +# hydro 4 f 11.6 +# hydro 3 p 6.2 +# hydro 3 d 5.6 +# hydro 5 g 17.6 +# hydro 1 s 0.75 +# "Third tier" - improvements: -2.83 meV to -0.50 meV +# ionic 2 p auto +# hydro 4 f 10.8 +# hydro 4 d 4.7 +# hydro 2 s 6.8 +# "Fourth tier" - improvements: -0.40 meV to -0.12 meV +# hydro 3 p 5 +# hydro 3 s 3.3 +# hydro 5 g 15.6 +# hydro 4 f 17.6 +# hydro 4 d 14 +# Further basis functions - -0.08 meV and below +# hydro 3 s 2.1 +# hydro 4 d 11.6 +# hydro 3 p 16 +# hydro 2 s 17.2 +################################################################################ +# +# FHI-aims code project +# VB, Fritz-Haber Institut, 2009 +# +# Suggested "light" defaults for H atom (to be pasted into control.in file) +# Be sure to double-check any results obtained with these settings for post-processing, +# e.g., with the "tight" defaults and larger basis sets. +# +################################################################################ + species H +# global species definitions + nucleus 1 + mass 1.00794 +# + l_hartree 4 +# + cut_pot 3.5 1.5 1.0 + basis_dep_cutoff 1e-4 +# + radial_base 24 5.0 + radial_multiplier 1 + angular_grids specified + division 0.2421 50 + division 0.3822 110 + division 0.4799 194 + division 0.5341 302 +# division 0.5626 434 +# division 0.5922 590 +# division 0.6542 770 +# division 0.6868 1202 +# outer_grid 770 + outer_grid 302 +################################################################################ +# +# Definition of "minimal" basis +# +################################################################################ +# valence basis states + valence 1 s 1. +# ion occupancy + ion_occ 1 s 0.5 +################################################################################ +# +# Suggested additional basis functions. For production calculations, +# uncomment them one after another (the most important basis functions are +# listed first). +# +# Basis constructed for dimers: 0.5 A, 0.7 A, 1.0 A, 1.5 A, 2.5 A +# +################################################################################ +# "First tier" - improvements: -1014.90 meV to -62.69 meV + hydro 2 s 2.1 + hydro 2 p 3.5 +# "Second tier" - improvements: -12.89 meV to -1.83 meV +# hydro 1 s 0.85 +# hydro 2 p 3.7 +# hydro 2 s 1.2 +# hydro 3 d 7 +# "Third tier" - improvements: -0.25 meV to -0.12 meV +# hydro 4 f 11.2 +# hydro 3 p 4.8 +# hydro 4 d 9 +# hydro 3 s 3.2 diff --git a/tests/test_base.py b/tests/test_base.py new file mode 100644 index 0000000..a22ceb3 --- /dev/null +++ b/tests/test_base.py @@ -0,0 +1,97 @@ +from dfttoolkit.base_parser import BaseParser +import pytest + + +@pytest.fixture +def elsi_csc(cwd): + yield f"{cwd}/fixtures/elsi_files/D_spin_01_kpt_000001.csc" + + +@pytest.fixture(autouse=True) +def base_parser(default_calc_dir, elsi_csc): + bp = BaseParser( + ["aims_out", "control_in", "elsi_out"], + aims_out=f"{default_calc_dir}/aims.out", + control_in=f"{default_calc_dir}/control.in", + elsi_out=elsi_csc, + ) + yield bp + + +def test_check_supported_file(default_calc_dir): + + with pytest.raises(ValueError): + BaseParser( + ["aims_out", "elsi_in"], + aims_out=f"{default_calc_dir}/aims.out", + control_in=f"{default_calc_dir}/control.in", + ) + + with pytest.raises(ValueError): + BaseParser( + ["aims.out", "control.in"], + aims_out=f"{default_calc_dir}/aims.out", + control_in=f"{default_calc_dir}/control.in", + ) + + +def test_check_file_exists(default_calc_dir): + with pytest.raises(FileNotFoundError): + BaseParser( + ["aims_out", "control_in"], + aims_out=f"{default_calc_dir}/aims.out", + control_in="./control.in", + ) + + +def test_store_file_paths(base_parser, default_calc_dir, cwd): + assert base_parser.file_paths == { + "aims_out": f"{default_calc_dir}/aims.out", + "control_in": f"{default_calc_dir}/control.in", + "elsi_out": f"{cwd}/fixtures/elsi_files/D_spin_01_kpt_000001.csc", + } + + +def test_read_binary_content(base_parser): + assert isinstance(base_parser.file_contents["elsi_out"], bytes) is True + + +def test_read_txt_content(elsi_csc, base_parser, default_calc_dir): + with open(elsi_csc, "rb") as f: + assert base_parser.file_contents["elsi_out"] == f.read() + + with open(f"{default_calc_dir}/aims.out", "r") as f: + assert base_parser.file_contents["aims_out"] == f.readlines() + + with open(f"{default_calc_dir}/control.in", "r") as f: + assert base_parser.file_contents["control_in"] == f.readlines() + + +def test__str__(base_parser, default_calc_dir): + base_parser.lines = base_parser.file_contents["aims_out"] + with open(f"{default_calc_dir}/aims.out", "r") as f: + ao_lines = f.readlines() + + assert str(base_parser) == "".join(ao_lines) + + base_parser.lines = base_parser.file_contents["control_in"] + with open(f"{default_calc_dir}/control.in", "r") as f: + ci_lines = f.readlines() + + assert str(base_parser) == "".join(ci_lines) + + +def test__str__error(base_parser): + # TODO maybe change to read the file as None or "" rather than just setting the attr + base_parser.lines = None + with pytest.raises(ValueError): + str(base_parser) + + base_parser.lines = "" + with pytest.raises(ValueError): + str(base_parser) + + +def test_properties(): + # TODO + pass diff --git a/tests/test_output.py b/tests/test_output.py index 0f5c9f6..d08505a 100644 --- a/tests/test_output.py +++ b/tests/test_output.py @@ -1,44 +1,22 @@ import os -import subprocess import numpy as np import pytest -import yaml from dfttoolkit.output import AimsOutput -from dfttoolkit.utils.file_utils import aims_bin_path_prompt class TestAimsOutput: + @property + def _aims_fixture_no(self) -> int: + return int(self.ao.path.split("/")[-2]) @pytest.fixture(params=range(1, 11), autouse=True) - def aims_out(self, request, run_aims): - - cwd = os.path.dirname(os.path.realpath(__file__)) - - # Run the FHI-aims calculations if the run-aims option is specified but not if - # they already exist. - # Force it to run if the run-aims option is "change_bin" - # run_aims fixture is defined in conftest.py - if request.param == 1 and run_aims is not False: - binary = aims_bin_path_prompt(run_aims, cwd) - subprocess.run(["bash", f"{cwd}/run_aims.sh", binary, str(run_aims)]) - aims_out_dir = "custom_bin_aims_calcs" - elif run_aims is not False: - aims_out_dir = "custom_bin_aims_calcs" - else: - aims_out_dir = "default_aims_calcs" + def aims_out(self, cwd, request, aims_calc_dir): self.ao = AimsOutput( - aims_out=f"{cwd}/fixtures/{aims_out_dir}/{str(request.param)}/aims.out" + aims_out=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}/aims.out" ) - with open(f"{cwd}/test_references.yaml", "r") as references: - self.ref_data = yaml.safe_load(references) - - @property - def _aims_fixture_no(self) -> int: - return int(self.ao.path.split("/")[-2]) - def test_get_number_of_atoms(self): if self._aims_fixture_no in [4, 6, 8, 10]: assert self.ao.get_number_of_atoms() == 2 @@ -64,12 +42,12 @@ def test_check_exit_normal(self): else: assert self.ao.check_exit_normal() is True - def test_get_time_per_scf(self): + def test_get_time_per_scf(self, ref_data): # Fail if the absolute tolerance between any values in test vs. reference array is # greater than 2e-3 assert np.allclose( self.ao.get_time_per_scf(), - self.ref_data["timings"][self._aims_fixture_no - 1], + ref_data["timings"][self._aims_fixture_no - 1], atol=2e-3, ) @@ -99,14 +77,14 @@ def test_get_change_of_total_energy_1(self): < 1e-8 ) - def test_get_change_of_total_energy_2(self): + def test_get_change_of_total_energy_2(self, ref_data): """Get every energy change""" # Fail if the absolute tolerance between any values in test vs. reference array is # greater than 1e-10 assert np.allclose( self.ao.get_change_of_total_energy(n_occurrence=None), - self.ref_data["energy_diffs"][self._aims_fixture_no - 1], + ref_data["energy_diffs"][self._aims_fixture_no - 1], atol=1e-8, ) @@ -142,7 +120,7 @@ def test_get_change_of_total_energy_3(self): # assert np.allclose( # self.ao.get_change_of_total_energy(n_occurrence=1), - # self.ref_data['all_energies'][self.aims_fixture_no(self.ao) - 1], + # ref_data['all_energies'][self.aims_fixture_no(self.ao) - 1], # atol=1e-10, # ) @@ -172,15 +150,11 @@ def test_check_spin_polarised(self): else: assert self.ao.check_spin_polarised() is False - def test_get_convergence_parameters(self): + def test_get_convergence_parameters(self, ref_data): if self._aims_fixture_no in [7, 8]: - assert ( - self.ao.get_convergence_parameters() == self.ref_data["conv_params"][1] - ) + assert self.ao.get_convergence_parameters() == ref_data["conv_params"][1] else: - assert ( - self.ao.get_convergence_parameters() == self.ref_data["conv_params"][0] - ) + assert self.ao.get_convergence_parameters() == ref_data["conv_params"][0] def test_get_final_energy(self): final_energies = [ @@ -236,25 +210,25 @@ def compare_n_initial_ks_states(): # TODO # def test_get_all_ks_eigenvalues(self): # if self._aims_fixture_no == 1: - # for key in self.ref_data["eigenvalues"].keys(): + # for key in ref_data["eigenvalues"].keys(): # # Check the values are within tolerance and that keys match # assert np.allclose( # self.ao.get_all_ks_eigenvalues()[key], - # self.ref_data["eigenvalues"][key], + # ref_data["eigenvalues"][key], # atol=1e-8, # ) # elif self._aims_fixture_no in [2, 3]: # spin_up, spin_down = self.ao.get_all_ks_eigenvalues() - # for key in self.ref_data["su_eigenvalues"].keys(): + # for key in ref_data["su_eigenvalues"].keys(): # # Check the values are within tolerance and that keys match # assert np.allclose( - # spin_up[key], self.ref_data["su_eigenvalues"][key], atol=1e-8 + # spin_up[key], ref_data["su_eigenvalues"][key], atol=1e-8 # ) # # Repeat for spin_down # assert np.allclose( - # spin_down[key], self.ref_data["sd_eigenvalues"][key], atol=1e-8 + # spin_down[key], ref_data["sd_eigenvalues"][key], atol=1e-8 # ) # else: @@ -264,13 +238,13 @@ def compare_n_initial_ks_states(): # TODO # def get_final_ks_eigenvalues_test(self): - def test_get_pert_soc_ks_eigenvalues(self): + def test_get_pert_soc_ks_eigenvalues(self, ref_data): if self._aims_fixture_no == 3: - for key in self.ref_data["pert_soc_eigenvalues"].keys(): + for key in ref_data["pert_soc_eigenvalues"].keys(): # Check the values are within tolerance and that keys match assert np.allclose( self.ao.get_pert_soc_ks_eigenvalues()[key], - self.ref_data["pert_soc_eigenvalues"][key], + ref_data["pert_soc_eigenvalues"][key], atol=1e-8, ) diff --git a/tests/test_parameters.py b/tests/test_parameters.py new file mode 100644 index 0000000..05a6d53 --- /dev/null +++ b/tests/test_parameters.py @@ -0,0 +1,60 @@ +import shutil + +import pytest +from dfttoolkit.parameters import AimsControl + + +class TestAimsControl: + @property + def aims_fixture_no(self) -> int: + return int(self.ac.path.split("/")[-2]) + + @pytest.fixture(params=range(1, 11), autouse=True) + def aims_control(self, cwd, request, aims_calc_dir): + self.ac = AimsControl( + control_in=f"{cwd}/fixtures/{aims_calc_dir}/{str(request.param)}" + "/control.in" + ) + + @pytest.fixture + def ref_files(self, cwd): + with open( + f"{cwd}/fixtures/manipulated_aims_files/{self.aims_fixture_no}/control.in", + "r", + ) as f: + yield f.readlines() + + def test_initialise_parameters(self, cwd): + with open( + f"{cwd}/fixtures/default_aims_calcs/{self.aims_fixture_no}/control.in", + "r", + ) as f: + assert self.ac.lines == f.readlines() + + assert self.ac.lines == self.ac.file_contents["control_in"] + assert self.ac.supported_files == ["control_in"] + assert self.ac.supported_files == self.ac._supported_files + assert self.ac.path.endswith("control.in") + + def test_remove_keywords_overwrite(self, tmp_dir, ref_files): + control_path = tmp_dir / "control.in" + shutil.copy(self.ac.path, control_path) + ac = AimsControl(control_in=str(control_path)) + ac.remove_keywords("xc", "relax_geometry", "k_grid", output="overwrite") + + assert "".join(ref_files) == control_path.read_text() + + def test_remove_keywords_print(self, capsys, ref_files): + self.ac.remove_keywords("xc", "relax_geometry", "k_grid", output="print") + out, err = capsys.readouterr() + + assert out == "".join(ref_files) + "\n" + assert err == "" + + def test_remove_keywords_return(self, ref_files): + control = self.ac.remove_keywords("xc", "relax_geometry", "k_grid") + assert control == ref_files + + def test_get_keywords(self, ref_data): + keywords = self.ac.get_keywords() + assert keywords == ref_data["keywords"][self.aims_fixture_no - 1] diff --git a/tests/test_references.yaml b/tests/test_references.yaml index 6bc4c34..c76687a 100644 --- a/tests/test_references.yaml +++ b/tests/test_references.yaml @@ -122,6 +122,48 @@ energy_diffs: 0.01499, -0.002865, 0.0002206, 7.186e-05, 6.018e-06] - [-2.158, -0.07087, 0.04834, 0.1184, -0.003943, 0.0103, -0.001032, 0.004801, 0.002519, 0.001141, 7.119e-06] +keywords: +- { "xc": "pbe", "output_level": "full" } +- { + "xc": "pbe", + "spin": "collinear", + "default_initial_moment": "1", + "output_level": "full", + } +- { + "xc": "pbe", + "spin": "collinear", + "default_initial_moment": "1", + "include_spin_orbit": "non_self_consistent", + "output_level": "full", + } +- { "xc": "pbe", "k_grid": "1 1 1" } +- { "xc": "pbe", "relax_geometry": "bfgs 5e-3" } +- { + "xc": "pbe", + "k_grid": "8 8 8", + "relax_geometry": "bfgs 5e-3", + "relax_unit_cell": "full", + } +- { + "xc": "pbe", + "relax_geometry": "bfgs 5e-3", + "sc_accuracy_rho": "1e-10", + "sc_accuracy_eev": "1e-6", + "sc_accuracy_etot": "1e-12", + "sc_accuracy_forces": "1e-8", + } +- { + "xc": "pbe", + "k_grid": "1 1 1", + "sc_iter_limit": "10", + "sc_accuracy_rho": "1e-10", + "sc_accuracy_eev": "1e-6", + "sc_accuracy_etot": "1e-12", + "sc_accuracy_forces": "1e-8", + } +- { "xc": "hse06 0.11", "hse_unit": "b" } +- { "xc": "hse06 0.11", "hse_unit": "b", "k_grid": "8 8 8" } pert_soc_eigenvalues: eigenvalue_eV: [-511.262291, -511.262291, -25.174078, -25.174077, -13.017798, -13.017797, -9.204901, -9.2049, -7.069313, -7.069308, 0.067805, 0.067807, 2.733286, 2.733288, diff --git a/tests/test_utils.py b/tests/test_utils.py index 8d57230..54d2f62 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -3,50 +3,45 @@ from dfttoolkit.utils.run_utils import no_repeat -class TestNoRepeat: +def test_specified_dir_not_found(): + @no_repeat(calc_dir="bogus") + def to_be_decorated(): + return True - calc_dir = ( - f"{os.path.dirname(os.path.realpath(__file__))}/fixtures/default_aims_calcs/1" - ) + with pytest.raises(ValueError) as excinfo: + to_be_decorated() - def test_specified_dir_not_found(self): - @no_repeat(calc_dir="bogus") - def to_be_decorated(): - return True - - with pytest.raises(ValueError) as excinfo: - to_be_decorated() - - assert "bogus is not a directory." == str(excinfo.value) - - @pytest.mark.parametrize( - ("calc_dir", "force", "expected"), - [ - ("./", False, True), - ( - f"{os.path.dirname(os.path.realpath(__file__))}/fixtures/default_aims_calcs/1", - True, - True, - ), - ], - ) - def test_default_dir_no_args(self, calc_dir, force, expected): - @no_repeat(calc_dir=calc_dir, force=force) - def to_be_decorated(): - return True + assert "bogus is not a directory." == str(excinfo.value) - assert to_be_decorated() == expected - def test_no_repeat(self, capfd): - @no_repeat(calc_dir=self.calc_dir) - def to_be_decorated(): - return True +@pytest.mark.parametrize( + ("default_calc_dir", "force", "expected"), + [ + ("./", False, True), + ( + f"{os.path.dirname(os.path.realpath(__file__))}/fixtures/default_aims_calcs/1", + True, + True, + ), + ], +) +def test_default_dir_no_args(default_calc_dir, force, expected): + @no_repeat(calc_dir=default_calc_dir, force=force) + def to_be_decorated(): + return True - to_be_decorated() + assert to_be_decorated() == expected - out, err = capfd.readouterr() - assert ( - out - == f"aims.out already exists in {self.calc_dir}. Skipping calculation.\n" - ) - assert err == "" + +def test_no_repeat(capfd, default_calc_dir): + @no_repeat(calc_dir=default_calc_dir) + def to_be_decorated(): + return True + + to_be_decorated() + + out, err = capfd.readouterr() + assert ( + out == f"aims.out already exists in {default_calc_dir}. Skipping calculation.\n" + ) + assert err == ""