generate lookup table for space groups

[elindgren]

Fixes #26

TODO

• Add unit test to ensure that keys always matches it's corresponding values

[elindgren]

I wrote a quick profiling script that just creates a SampleModel and applies the symmetry constraints. This operation takes from 0.1s -> 0.007s. It seems like the next biggest bottleneck is the call to sympify.

Profiling results on develop

Profiling results on the feature branch

Profiling script

from easydiffraction import SampleModel
import cProfile
import pstats

def main():
    model = SampleModel('hs')
    model.space_group.name_h_m = 'R -3 m'
    model.space_group.it_coordinate_system_code = 'h'
    model.cell.length_a = 6.9
    model.cell.length_c = 14.1
    model.atom_sites.add('Zn', 'Zn', 0, 0, 0.5, wyckoff_letter='b', b_iso=0.5)
    model.atom_sites.add('Cu', 'Cu', 0.5, 0, 0, wyckoff_letter='e', b_iso=0.5)
    model.atom_sites.add('O', 'O', 0.21, -0.21, 0.06, wyckoff_letter='h', b_iso=0.5)
    model.atom_sites.add('Cl', 'Cl', 0, 0, 0.197, wyckoff_letter='c', b_iso=0.5)
    model.atom_sites.add('H', '2H', 0.13, -0.13, 0.08, wyckoff_letter='h', b_iso=0.5)
    model.apply_symmetry_constraints()

if __name__ == "__main__":
    with cProfile.Profile() as pr:
        main()
    stats = pstats.Stats(pr)
    stats.dump_stats("profile_output.prof")

[elindgren]

I also benchmarked a more thorough example, which actually performs a fit. The tabulated values helps a lot, the fit takes 42s on develop but only ~8s on the feature branch. On develop, a whopping 35s is taken up by cryspy computing the symmetry operations. On the feature branch, symmetry operations still take up 2s of the runtime, because of sympy.

Profiling results on develop

Profiling results on the feature branch

Benchmarking script

import cProfile
import pstats
from easydiffraction import (
    Project,
    SampleModel,
    Experiment
)

def prebench():
    # Create and configure sample model
    model = SampleModel('hs')
    model.space_group.name_h_m = 'R -3 m'
    model.space_group.it_coordinate_system_code = 'h'
    model.cell.length_a = 6.9
    model.cell.length_c = 14.1
    model.atom_sites.add('Zn', 'Zn', 0, 0, 0.5, wyckoff_letter='b', b_iso=0.5)
    model.atom_sites.add('Cu', 'Cu', 0.5, 0, 0, wyckoff_letter='e', b_iso=0.5)
    model.atom_sites.add('O', 'O', 0.21, -0.21, 0.06, wyckoff_letter='h', b_iso=0.5)
    model.atom_sites.add('Cl', 'Cl', 0, 0, 0.197, wyckoff_letter='c', b_iso=0.5)
    model.atom_sites.add('H', '2H', 0.13, -0.13, 0.08, wyckoff_letter='h', b_iso=0.5)
    model.show_as_cif()
    model.apply_symmetry_constraints()
    model.show_as_cif()

    # Create and configure experiment
    expt = Experiment('hrpt', data_path='examples/data/hrpt_hs.xye')
    expt.instrument.setup_wavelength = 1.89
    expt.instrument.calib_twotheta_offset = 0.0
    expt.peak.broad_gauss_u = 0.1
    expt.peak.broad_gauss_v = -0.2
    expt.peak.broad_gauss_w = 0.2
    expt.peak.broad_lorentz_x = 0.0
    expt.peak.broad_lorentz_y = 0
    expt.linked_phases.add('hs', scale=0.5)
    expt.background.add(x=4.4196, y=500)
    expt.background.add(x=6.6207, y=500)
    expt.background.add(x=10.4918, y=500)
    expt.background.add(x=15.4634, y=500)
    expt.background.add(x=45.6041, y=500)
    expt.background.add(x=74.6844, y=500)
    expt.background.add(x=103.4187, y=500)
    expt.background.add(x=121.6311, y=500)
    expt.background.add(x=159.4116, y=500)
    expt.show_as_cif()

    # Create project and add sample model and experiments
    project = Project()
    project.sample_models.add(model)
    project.experiments.add(expt)

    # Set calculator, minimizer and fit mode
    project.analysis.current_calculator = 'cryspy'
    project.analysis.current_minimizer = 'lmfit (leastsq)'

    # Compare measured and calculated patterns
    project.analysis.show_meas_vs_calc_chart('hrpt', 48, 51)

    # ------------ 1st fitting ------------

    # Define free parameters
    model.cell.length_a.free = True
    model.cell.length_c.free = True
    expt.linked_phases['hs'].scale.free = True
    expt.instrument.calib_twotheta_offset.free = True
    project.analysis.show_free_params()
    return project

def main(project):
    # Start fitting
    project.analysis.fit()

if __name__ == "__main__":
    project = prebench()
    with cProfile.Profile() as pr:
        main(project)
    stats = pstats.Stats(pr)
    stats.dump_stats("profile_output.prof")

[elindgren]

@AndrewSazonov this is ready to go

[AndrewSazonov]

Looks good to me