diff --git a/atomdb/datasets/orca/__init__.py b/atomdb/datasets/orca/__init__.py new file mode 100644 index 00000000..94d29b6b --- /dev/null +++ b/atomdb/datasets/orca/__init__.py @@ -0,0 +1,16 @@ +# This file is part of AtomDB. +# +# AtomDB is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free +# Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# AtomDB is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +# for more details. +# +# You should have received a copy of the GNU General Public License +# along with AtomDB. If not, see . + +r"""ORCA dataset.""" diff --git a/atomdb/datasets/orca/run.py b/atomdb/datasets/orca/run.py new file mode 100644 index 00000000..32b7a2a4 --- /dev/null +++ b/atomdb/datasets/orca/run.py @@ -0,0 +1,302 @@ +# This file is part of AtomDB. +# +# AtomDB is free software: you can redistribute it and/or modify it under +# the terms of the GNU General Public License as published by the Free +# Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# AtomDB is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +# for more details. +# +# You should have received a copy of the GNU General Public License +# along with AtomDB. If not, see . + +r"""ORCA density compile function.""" + +import os + +import numpy as np +from gbasis.evals.density import evaluate_density as eval_dens +from gbasis.evals.density import evaluate_posdef_kinetic_energy_density as eval_pd_ked +from gbasis.evals.eval import evaluate_basis +from gbasis.wrappers import from_iodata +from grid.atomgrid import AtomGrid +from grid.onedgrid import UniformInteger +from grid.rtransform import ExpRTransform +from iodata import load_one, IOData + +import atomdb +from atomdb.datasets.tools import ( + eval_orb_ked, + eval_orbs_density, + eval_orbs_radial_d_density, + eval_orbs_radial_dd_density, + eval_radial_d_density, + eval_radial_dd_density, +) +from atomdb.periodic import Element + +__all__ = [ + "run", +] + + +# Parameters to generate an atomic grid from uniform radial grid +# Use 170 points, lmax = 21 for the Lebedev grid since our basis +# don't go beyond l=10 in the spherical harmonics. +BOUND = (1e-30, 2e1) # (r_min, r_max) + +NPOINTS = 1000 + +SIZE = 175 # Lebedev grid sizes + +DEGREE = 21 # Lebedev grid degrees + + +DOCSTRING = """ORCA basis densities (wb97m-d3bj) Dataset + +Electronic structure and density properties evaluated with def2-tzvppd basis set + +""" +def _load_molden(n_atom: int, element: str, n_elec: int, multi: int, basis_name: str, data_path: str) -> IOData: + r"""Load ORCA molden.input file and return the iodata object + + This function finds the molden file in the data directory corresponding to the given parameters, + loads it and returns the iodata object. + + Parameters + ---------- + n_atom : int + Atomic number + element : str + Chemical symbol of the species + n_elec : int + Number of electrons + multi : int + Multiplicity + basis_name : str + Basis set name + data_path : str + Path to the data directory + + Returns + ------- + iodata : iodata.IOData + Iodata object containing the data from the molden file + """ + + bname = basis_name.lower().replace("-", "").replace("*", "p").replace("+", "d") + prefix = f"{str(n_atom).zfill(4)}" + tag = f"q{str(n_atom-n_elec).zfill(3)}_m0{multi}" + method = f"k00_force_{bname}" + moldenpath = os.path.join(data_path, f"orca/raw/{prefix}_{tag}_{method}.molden.input") + return load_one(moldenpath) + + +def run(elem, charge, mult, nexc, dataset, datapath): + r"""Compile the AtomDB database entry for densities from an ORCA calculation.""" + # Check arguments + if nexc != 0: + raise ValueError("Nonzero value of `nexc` is not currently supported") + + # Set up internal variables + elem = atomdb.element_symbol(elem) + atnum = atomdb.element_number(elem) + nelec = atnum - charge + nspin = mult - 1 + n_up = (nelec + nspin) // 2 + n_dn = (nelec - nspin) // 2 + + # Load data from molden + obasis_name = "def2-tzvppd" + if nelec == 0: + # For zero-electron case. use 1-electron case as a base + data = _load_molden(atnum, elem, 1, 2, obasis_name, datapath) + else: + data = _load_molden(atnum, elem, nelec, mult, obasis_name, datapath) + + # Unrestricted Hartree-Fock SCF results + energy = data.energy + norba = data.mo.norba + mo_e_up = data.mo.energies[:norba] + mo_e_dn = data.mo.energies[norba:] + occs_up = data.mo.occs[:norba] + occs_dn = data.mo.occs[norba:] + mo_coeffs = data.mo.coeffs # ndarray(nbasis, norba + norbb) + coeffs_a = mo_coeffs[:, :norba] + coeffs_b = mo_coeffs[:, norba:] + + # check for inconsistencies in filenames + if nelec != 0 and not np.allclose([n_up, n_dn], [sum(occs_up), sum(occs_dn)]): + raise ValueError(f"Inconsistent data in molden file for N: {atnum}, M: {mult} CH: {charge}") + + # Prepare data for computing Species properties + # density matrix in AO basis + dm1_up = np.dot(coeffs_a * occs_up, coeffs_a.T) + dm1_dn = np.dot(coeffs_b * occs_dn, coeffs_b.T) + dm1_tot = dm1_up + dm1_dn + + # Make grid + onedg = UniformInteger(NPOINTS) # number of uniform grid points. + rgrid = ExpRTransform(*BOUND).transform_1d_grid(onedg) # radial grid + atgrid = AtomGrid(rgrid, degrees=[DEGREE], sizes=[SIZE], center=np.array([0.0, 0.0, 0.0])) + + # Evaluate properties on the grid: + # -------------------------------- + # total and spin-up orbital, and spin-down orbital densities + obasis = from_iodata(data) + orb_eval = evaluate_basis(obasis, atgrid.points, transform=None) + orb_dens_up = eval_orbs_density(dm1_up, orb_eval) + orb_dens_dn = eval_orbs_density(dm1_dn, orb_eval) + dens_tot = eval_dens(dm1_tot, obasis, atgrid.points, transform=None) + + # total, spin-up orbital, and spin-down orbital first (radial) derivatives of the density + d_dens_tot = eval_radial_d_density(dm1_tot, obasis, atgrid.points) + orb_d_dens_up = eval_orbs_radial_d_density(dm1_up, obasis, atgrid.points, transform=None) + orb_d_dens_dn = eval_orbs_radial_d_density(dm1_dn, obasis, atgrid.points, transform=None) + + # total, spin-up orbital, and spin-down orbital second (radial) derivatives of the density + dd_dens_tot = eval_radial_dd_density(dm1_tot, obasis, atgrid.points) + orb_dd_dens_up = eval_orbs_radial_dd_density(dm1_up, obasis, atgrid.points, transform=None) + orb_dd_dens_dn = eval_orbs_radial_dd_density(dm1_dn, obasis, atgrid.points, transform=None) + + # total, spin-up orbital, and spin-down orbital kinetic energy densities + ked_tot = eval_pd_ked(dm1_tot, obasis, atgrid.points, transform=None) + orb_ked_up = eval_orb_ked(dm1_up, obasis, atgrid.points, transform=None) + orb_ked_dn = eval_orb_ked(dm1_dn, obasis, atgrid.points, transform=None) + + # Spherically average properties: + # -------------------------------- + # total, spin-up orbital, and spin-down orbital densities + dens_spherical_avg = atgrid.spherical_average(dens_tot) + dens_splines_up = [atgrid.spherical_average(dens) for dens in orb_dens_up] + dens_splines_dn = [atgrid.spherical_average(dens) for dens in orb_dens_dn] + + # total, spin-up orbital, and spin-down orbital radial derivatives of the density + d_dens_spherical_avg = atgrid.spherical_average(d_dens_tot) + d_dens_splines_up = [atgrid.spherical_average(d_dens) for d_dens in orb_d_dens_up] + d_dens_splines_dn = [atgrid.spherical_average(d_dens) for d_dens in orb_d_dens_dn] + + # total, spin-up orbital, and spin-down orbital radial second derivatives of the density + dd_dens_spherical_avg = atgrid.spherical_average(dd_dens_tot) + dd_dens_splines_up = [atgrid.spherical_average(dd_dens) for dd_dens in orb_dd_dens_up] + dd_dens_splines_dn = [atgrid.spherical_average(dd_dens) for dd_dens in orb_dd_dens_dn] + + # total, spin-up orbital, and spin-down orbital kinetic energy densities + ked_spherical_avg = atgrid.spherical_average(ked_tot) + ked_splines_up = [atgrid.spherical_average(dens) for dens in orb_ked_up] + ked_splines_dn = [atgrid.spherical_average(dens) for dens in orb_ked_dn] + + # Evaluate interpolated densities in uniform radial grid: + # ------------------------------------------------------- + rs = rgrid.points + # total, spin-up orbital, and spin-down orbital densities + dens_avg_tot = dens_spherical_avg(rs) + orb_dens_avg_up = np.array([spline(rs) for spline in dens_splines_up]) + orb_dens_avg_dn = np.array([spline(rs) for spline in dens_splines_dn]) + + # total, spin-up orbital, and spin-down orbital radial derivatives of the density + d_dens_avg_tot = d_dens_spherical_avg(rs) + orb_d_dens_avg_up = np.array([spline(rs) for spline in d_dens_splines_up]) + orb_d_dens_avg_dn = np.array([spline(rs) for spline in d_dens_splines_dn]) + + # total, spin-up orbital, and spin-down orbital radial second derivatives of the density + dd_dens_avg_tot = dd_dens_spherical_avg(rs) + orb_dd_dens_avg_up = np.array([spline(rs) for spline in dd_dens_splines_up]) + orb_dd_dens_avg_dn = np.array([spline(rs) for spline in dd_dens_splines_dn]) + + # total, spin-up orbital, and spin-down orbital kinetic energy densities + ked_avg_tot = ked_spherical_avg(rs) + orb_ked_avg_up = np.array([spline(rs) for spline in ked_splines_up]) + orb_ked_avg_dn = np.array([spline(rs) for spline in ked_splines_dn]) + + # Get information about the element + atom = Element(elem) + atmass = atom.mass + cov_radius, vdw_radius, at_radius, polarizability, dispersion = [ + None, + ] * 5 + # overwrite values for neutral atomic species + if charge == 0: + cov_radius, vdw_radius, at_radius = (atom.cov_radius, atom.vdw_radius, atom.at_radius) + polarizability = atom.pold + dispersion = {"C6": atom.c6} + + # Conceptual-DFT properties (WIP) + # NOTE: Only the alpha component of the MOs is used below + # NOTE: Handle zero-electron case here + mo_energy_occ_up = mo_e_up[:n_up] + mo_energy_virt_up = mo_e_up[n_up:] + ip = -mo_energy_occ_up[-1] if nelec != 0 else 0 # - energy_HOMO_alpha + ea = -mo_energy_virt_up[0] if nelec != 0 else 0 # - energy_LUMO_alpha + mu = None + eta = None + + # Set appropriate values to zero for zero-electron case + if nelec == 0: + energy = 0.0 + mo_e_up[...] = 0 + mo_e_dn[...] = 0 + occs_up[...] = 0 + occs_dn[...] = 0 + # Density + orb_dens_avg_up[...] = 0 + orb_dens_avg_dn[...] = 0 + dens_avg_tot[...] = 0 + # Density gradient + orb_d_dens_avg_up[...] = 0 + orb_d_dens_avg_dn[...] = 0 + d_dens_avg_tot[...] = 0 + # Density laplacian + orb_dd_dens_avg_up[...] = 0 + orb_dd_dens_avg_dn[...] = 0 + dd_dens_avg_tot[...] = 0 + # KED + orb_ked_avg_up[...] = 0 + orb_ked_avg_dn[...] = 0 + ked_avg_tot[...] = 0 + + # Return Species instance + fields = dict( + elem=elem, + atnum=atnum, + obasis_name=obasis_name, + nelec=nelec, + nspin=nspin, + nexc=nexc, + atmass=atmass, + cov_radius=cov_radius, + vdw_radius=vdw_radius, + at_radius=at_radius, + polarizability=polarizability, + dispersion=dispersion, + energy=energy, + mo_energy_a=mo_e_up, + mo_energy_b=mo_e_dn, + mo_occs_a=occs_up, + mo_occs_b=occs_dn, + ip=ip, + # ea=ea, + mu=mu, + eta=eta, + rs=rs, + # Density + mo_dens_a=orb_dens_avg_up.flatten(), + mo_dens_b=orb_dens_avg_dn.flatten(), + dens_tot=dens_avg_tot, + # Density gradient + mo_d_dens_a=orb_d_dens_avg_up.flatten(), + mo_d_dens_b=orb_d_dens_avg_dn.flatten(), + d_dens_tot=d_dens_avg_tot, + # Density laplacian + mo_dd_dens_a=orb_dd_dens_avg_up.flatten(), + mo_dd_dens_b=orb_dd_dens_avg_dn.flatten(), + dd_dens_tot=dd_dens_avg_tot, + # KED + mo_ked_a=orb_ked_avg_up.flatten(), + mo_ked_b=orb_ked_avg_dn.flatten(), + ked_tot=ked_avg_tot, + ) + return atomdb.Species(dataset, fields) diff --git a/atomdb/test/data/orca/raw/0006_q000_m03_k00_force_def2tzvppd.molden.input b/atomdb/test/data/orca/raw/0006_q000_m03_k00_force_def2tzvppd.molden.input new file mode 100644 index 00000000..1fd8f98b --- /dev/null +++ b/atomdb/test/data/orca/raw/0006_q000_m03_k00_force_def2tzvppd.molden.input @@ -0,0 +1,3082 @@ +[Molden Format] +[Title] + Molden file created by orca_2mkl for BaseName=orca + +[Atoms] AU +C 1 6 0.0000000000 0.0000000000 0.0000000000 +[GTO] + 1 0 +s 6 1.0 + 13575.3496820000 0.5435905310 + 2035.2333680000 1.0145543947 + 463.2256235900 1.7315731970 + 131.2001959800 2.6910376290 + 42.8530158910 3.6044547126 + 15.5841857660 3.7025556986 +s 2 1.0 + 6.2067138508 1.8383540830 + 2.5764896527 0.5447575605 +s 1 1.0 + 0.5769633942 0.4718145038 +s 1 1.0 + 0.2297283136 0.2364944676 +s 1 1.0 + 0.0951644400 0.1221141848 +p 4 1.0 + 34.6972322440 1.3596651507 + 7.9582622826 1.4512589486 + 2.3780826883 1.2709231419 + 0.8143320818 0.8025721189 +p 1 1.0 + 0.2888754725 0.3018758868 +p 1 1.0 + 0.1005682367 0.0807265016 +d 1 1.0 + 1.0970000000 3.3522135855 +d 1 1.0 + 0.3180000000 0.3838994974 +f 1 1.0 + 0.7610000000 3.0840084332 +s 1 1.0 + 0.0484754014 0.0736293816 +d 1 1.0 + 0.0909853364 0.0429704639 + +[5D] +[7F] +[9G] +[MO] + Sym= 1a + Ene= -1.04784547675924E+01 + Spin= Alpha + Occup= 1.000000 + 1 0.467987629413 + 2 0.609469996732 + 3 0.030761091408 + 4 -0.021649229962 + 5 0.014355431218 + 6 0.000000005011 + 7 0.000000010025 + 8 0.000000007955 + 9 -0.000000002873 + 10 -0.000000008013 + 11 -0.000000005542 + 12 0.000000000959 + 13 0.000000002071 + 14 0.000000001589 + 15 0.000188331871 + 16 -0.000442207403 + 17 0.000221728660 + 18 -0.000328433608 + 19 0.000439985835 + 20 -0.000069551059 + 21 0.000163308513 + 22 -0.000081885305 + 23 0.000121290762 + 24 -0.000162488037 + 25 -0.000000000266 + 26 -0.000000000098 + 27 0.000000000039 + 28 0.000000000162 + 29 -0.000000000346 + 30 -0.000000000034 + 31 0.000000000318 + 32 -0.005404716742 + 33 0.000039200928 + 34 -0.000092043345 + 35 0.000046151706 + 36 -0.000068362683 + 37 0.000091581094 + Sym= 1a + Ene= -6.97014718933022E-01 + Spin= Alpha + Occup= 1.000000 + 1 0.114027266167 + 2 0.249047501680 + 3 -0.440292020626 + 4 -0.508604288693 + 5 -0.178415443118 + 6 -0.000000432428 + 7 -0.000000085266 + 8 -0.000000348692 + 9 -0.000000412017 + 10 -0.000000077404 + 11 -0.000000330426 + 12 -0.000000064575 + 13 0.000000108009 + 14 0.000000000063 + 15 -0.000858259442 + 16 0.002015259684 + 17 -0.001010484333 + 18 0.001496720022 + 19 -0.002005135218 + 20 -0.000555069401 + 21 0.001303259072 + 22 -0.000653449143 + 23 0.000968006230 + 24 -0.001296710319 + 25 0.000000008137 + 26 0.000000002841 + 27 -0.000000001208 + 28 -0.000000006354 + 29 0.000000010678 + 30 0.000000000240 + 31 -0.000000011888 + 32 -0.005736556806 + 33 -0.001175067832 + 34 0.002759004406 + 35 -0.001383382372 + 36 0.002049214081 + 37 -0.002745148331 + Sym= 1a + Ene= -3.63793450960664E-01 + Spin= Alpha + Occup= 1.000000 + 1 0.000000008232 + 2 0.000000017342 + 3 -0.000000007170 + 4 -0.000000027522 + 5 -0.000000064750 + 6 0.282423150998 + 7 0.270663197239 + 8 -0.291127221179 + 9 0.245251452288 + 10 0.235039660623 + 11 -0.252810292203 + 12 0.164582975843 + 13 0.157730223251 + 14 -0.169655700774 + 15 -0.000000075971 + 16 0.000000007009 + 17 -0.000000005188 + 18 -0.000000006383 + 19 0.000000058679 + 20 -0.000000181281 + 21 0.000000019698 + 22 -0.000000009715 + 23 -0.000000026299 + 24 0.000000146750 + 25 0.000092344849 + 26 -0.000843134684 + 27 0.000369359324 + 28 0.000353791068 + 29 0.000733654524 + 30 -0.001028080226 + 31 0.000171643390 + 32 -0.000000078581 + 33 -0.000000150695 + 34 0.000000022969 + 35 0.000000003521 + 36 -0.000000033846 + 37 0.000000125811 + Sym= 1a + Ene= -3.63793383903090E-01 + Spin= Alpha + Occup= 1.000000 + 1 0.000000028430 + 2 0.000000059933 + 3 -0.000000025374 + 4 -0.000000094436 + 5 -0.000000224057 + 6 0.007804758141 + 7 0.353280192593 + 8 0.336018711156 + 9 0.006777537230 + 10 0.306782863269 + 11 0.291793283408 + 12 0.004548278382 + 13 0.205875550306 + 14 0.195816349586 + 15 0.000000019883 + 16 0.000000032207 + 17 0.000000078672 + 18 -0.000000039685 + 19 0.000000028040 + 20 0.000000045570 + 21 0.000000075556 + 22 0.000000215969 + 23 -0.000000116611 + 24 0.000000080847 + 25 -0.000106599691 + 26 0.000929892607 + 27 -0.000512515799 + 28 0.000761334879 + 29 0.000026345382 + 30 -0.000766749430 + 31 -0.000546416332 + 32 -0.000000269688 + 33 0.000000029378 + 34 0.000000074776 + 35 0.000000221843 + 36 -0.000000125720 + 37 0.000000084530 + Sym= 1a + Ene= -6.29567406754203E-02 + Spin= Alpha + Occup= 0.000000 + 1 -0.000000080640 + 2 -0.000000170701 + 3 0.000000261471 + 4 0.000000332704 + 5 0.000000108363 + 6 -0.349705619722 + 7 0.175344947627 + 8 -0.176229821117 + 9 -0.302774124771 + 10 0.151813364026 + 11 -0.152579513389 + 12 -0.334978102909 + 13 0.167960881314 + 14 -0.168808544048 + 15 0.000000001377 + 16 -0.000000049832 + 17 0.000000011254 + 18 -0.000000041968 + 19 0.000000010497 + 20 -0.000000002317 + 21 -0.000000065359 + 22 0.000000011669 + 23 -0.000000055897 + 24 0.000000005433 + 25 -0.001254366773 + 26 -0.000221187086 + 27 0.000110924210 + 28 0.001120264828 + 29 -0.001500745507 + 30 -0.000297894912 + 31 0.001670800515 + 32 0.000000334420 + 33 -0.000000024493 + 34 -0.000000030485 + 35 -0.000000010645 + 36 -0.000000032037 + 37 -0.000000043482 + Sym= 1a + Ene= 5.82818579543061E-02 + Spin= Alpha + Occup= 0.000000 + 1 -0.028683097303 + 2 -0.072123451934 + 3 0.266879234187 + 4 -0.451618092331 + 5 2.237215807914 + 6 -0.000000063347 + 7 -0.000000030268 + 8 -0.000000058685 + 9 -0.000000026909 + 10 0.000000044259 + 11 -0.000000000266 + 12 -0.000000210983 + 13 -0.000000228728 + 14 -0.000000250872 + 15 0.000383361756 + 16 -0.000900151596 + 17 0.000451347840 + 18 -0.000668548548 + 19 0.000895629051 + 20 -0.001883146176 + 21 0.004421499115 + 22 -0.002216975986 + 23 0.003284025912 + 24 -0.004399298118 + 25 -0.000000002245 + 26 -0.000000000309 + 27 0.000000000123 + 28 0.000000002273 + 29 -0.000000002767 + 30 -0.000000000752 + 31 0.000000002935 + 32 -2.547313966770 + 33 0.007758321927 + 34 -0.018216036091 + 35 0.009133666014 + 36 -0.013529768340 + 37 0.018124568175 + Sym= 1a + Ene= 2.43544795672565E-01 + Spin= Alpha + Occup= 0.000000 + 1 0.000119728055 + 2 -0.001328366888 + 3 0.027739792979 + 4 -0.128656433258 + 5 0.260486446958 + 6 0.000000112077 + 7 0.000000086998 + 8 0.000000118568 + 9 0.000000276003 + 10 0.000000053506 + 11 0.000000221951 + 12 -0.000000430568 + 13 0.000000070603 + 14 -0.000000279057 + 15 -0.008191956757 + 16 0.019234109339 + 17 -0.009644128568 + 18 0.014285976304 + 19 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-0.000459727645 + 20 0.000134500672 + 21 -0.000315798770 + 22 0.000158344008 + 23 -0.000234556212 + 24 0.000314213054 + 25 0.000000000070 + 26 -0.000000000072 + 27 0.000000000045 + 28 -0.000000000167 + 29 0.000000000050 + 30 0.000000000147 + 31 -0.000000000022 + 32 0.450297615549 + 33 -0.000049597581 + 34 0.000116451811 + 35 -0.000058389857 + 36 0.000086493400 + 37 -0.000115867078 diff --git a/atomdb/test/test_orca.py b/atomdb/test/test_orca.py new file mode 100644 index 00000000..a5ff3fdf --- /dev/null +++ b/atomdb/test/test_orca.py @@ -0,0 +1,22 @@ +import pytest +from importlib import import_module +from importlib_resources import files +import os + +from atomdb import Species + + +TEST_DATAPATH = files("atomdb.test.data") +TEST_DATAPATH = os.fspath(TEST_DATAPATH._paths[0]) + +@pytest.mark.slow +@pytest.mark.parametrize( + "element, charge, mult, dataset", [("C", 0, 3, "orca")] +) +def test_compile(element, charge, mult, dataset): + submodule = import_module(f"atomdb.datasets.orca.run") + # Compile the Species instance + species = submodule.run(element, charge, mult, 0, dataset, TEST_DATAPATH) + assert isinstance(species, Species) + + diff --git a/pyproject.toml b/pyproject.toml index 8b9f82a9..e3e1f6cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -113,7 +113,8 @@ extend-exclude = ["doc/*", "doc/*/*"] [tool.pytest.ini_options] minversion = "7.0" testpaths = ["test"] -addopts = "-m 'not dev'" +addopts = "-m 'not dev and not slow'" markers = [ "dev: mark a developer test, needs extra dependencies.", + "slow: mark a test as slow.", ]