Source code for pysisyphus.benchmarks.Benchmark

from pysisyphus.helpers import Geometry
from pysisyphus.helpers import geom_loader
from import *

[docs] class Benchmark: data_funcs = { "baker": get_baker_data, "baker_ts": get_baker_ts_data, "s22": get_s22_data, "zimmerman": get_zimmerman_data, "zimmerman_xtb": get_zimmerman_xtb_data, "birkholz_rx": get_birkholz_rx_data, "xtb_rx": get_xtb_rx_data, "precon_pos_rot": get_precon_pos_rot_data, } def __init__( self, name, exclude=None, inv_exclude=False, only=None, coord_type="cart", calc_getter=None, ): = name if exclude is None: exclude = tuple() if only is None: only = tuple() self.exclude = exclude if isinstance(only, int): only = (only, ) self.only = only self.coord_type = coord_type self.calc_getter = calc_getter self.data_func = self.data_funcs[] self.prefix, = self.data_func() self.fns = [fn for fn, *_ in] def exclude_from(iterable): self.exclude = [ id_ for id_, _ in enumerate( if id_ not in iterable ] # Only takes precedence if self.only: exclude_from(self.only) elif inv_exclude: exclude_from(self.exclude)
[docs] def get_geoms(self, id_, set_calculator=True): fn, charge, mult, ref_energy =[id_] geoms = geom_loader(self.prefix + fn, coord_type=self.coord_type) # Make atleast 1d if isinstance(geoms, Geometry): geoms = (geoms, ) for geom in geoms: if set_calculator and self.calc_getter: geom.set_calculator(self.calc_getter(charge=charge, mult=mult)) # Single geomtries are returned directly if len(geoms) == 1: geoms = geoms[0] return geoms
def __iter__(self): self._id = 0 return self def __next__(self): """Iterating directly over a Benchmark object, e.g., in pytest.mark.parametrize will give problems when calc_getter is set, but the calculator is not available/installed. Pytest will eagerly collect all geoms, and in this process the calculators will be created. But when the calculator command is not available, a SystemExit occur. In theses cases it may be better to leave the calc_getter and iterate over Benchmark.geom_iter, and to construct the calculators manually. """ while self._id < len( if self._id in self.exclude: self._id += 1 continue fn, *_, ref_energy =[self._id] geoms = self.get_geoms(self._id) self._id += 1 return fn, geoms, ref_energy raise StopIteration @property def geom_iter(self): for i, fn in enumerate(self.fns): if i in self.exclude: continue fn, charge, mult, ref_energy =[i] geoms = self.get_geoms(i, set_calculator=False) yield fn, geoms, charge, mult, ref_energy @property def geoms(self): for i, fn in enumerate(self.fns): if i in self.exclude: continue yield self.get_geoms(i)