From 4019fadd6567f4433ba6f62c77d39f6f5b6c4632 Mon Sep 17 00:00:00 2001 From: Ask Hjorth Larsen Date: Fri, 4 Feb 2022 14:09:08 +0100 Subject: [PATCH 1/4] prevent computations from running at import time --- ase/optimize/test/neb.py | 86 ++++++++++---------- ase/optimize/test/systems.py | 147 +++++++++++++++++------------------ 2 files changed, 117 insertions(+), 116 deletions(-) diff --git a/ase/optimize/test/neb.py b/ase/optimize/test/neb.py index 100b8c853..d9ad1b976 100644 --- a/ase/optimize/test/neb.py +++ b/ase/optimize/test/neb.py @@ -4,43 +4,49 @@ from ase.calculators.emt import EMT from ase.neb import NEB from ase.build import fcc100, add_adsorbate -# 2x2-Al(001) surface with 3 layers and an -# Au atom adsorbed in a hollow site: -slab = fcc100('Al', size=(2, 2, 3)) -add_adsorbate(slab, 'Au', 1.7, 'hollow') -slab.center(axis=2, vacuum=4.0) - -# Fix second and third layers: -mask = [atom.tag > 1 for atom in slab] -slab.set_constraint(FixAtoms(mask=mask)) - -# Use EMT potential: -slab.calc = EMT() - -# Initial state: -qn = QuasiNewton(slab, logfile=None) -qn.run(fmax=0.05) -initial = slab.copy() - -# Final state: -slab[-1].x += slab.get_cell()[0, 0] / 2 -qn = QuasiNewton(slab, logfile=None) -qn.run(fmax=0.05) -final = slab.copy() - -# Setup a NEB calculation -constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial]) - -images = [initial] -for i in range(3): - image = initial.copy() - image.set_constraint(constraint) - images.append(image) - -images.append(final) - -neb = NEB(images) -neb.interpolate() - -for image in neb.images[1:-1]: - image.calc = EMT() + +def main(): + # 2x2-Al(001) surface with 3 layers and an + # Au atom adsorbed in a hollow site: + slab = fcc100('Al', size=(2, 2, 3)) + add_adsorbate(slab, 'Au', 1.7, 'hollow') + slab.center(axis=2, vacuum=4.0) + + # Fix second and third layers: + mask = [atom.tag > 1 for atom in slab] + slab.set_constraint(FixAtoms(mask=mask)) + + # Use EMT potential: + slab.calc = EMT() + + # Initial state: + qn = QuasiNewton(slab, logfile=None) + qn.run(fmax=0.05) + initial = slab.copy() + + # Final state: + slab[-1].x += slab.get_cell()[0, 0] / 2 + qn = QuasiNewton(slab, logfile=None) + qn.run(fmax=0.05) + final = slab.copy() + + # Setup a NEB calculation + constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial]) + + images = [initial] + for i in range(3): + image = initial.copy() + image.set_constraint(constraint) + images.append(image) + + images.append(final) + + neb = NEB(images) + neb.interpolate() + + for image in neb.images[1:-1]: + image.calc = EMT() + + +if __name__ == '__main__': + main() diff --git a/ase/optimize/test/systems.py b/ase/optimize/test/systems.py index df75355d8..3014efe37 100644 --- a/ase/optimize/test/systems.py +++ b/ase/optimize/test/systems.py @@ -7,92 +7,87 @@ from ase.constraints import FixAtoms from ase.lattice.cubic import FaceCenteredCubic from ase.cluster import wulff_construction -systems = [] -cell = (5, 5, 5) -atoms = Atoms('H2', [(0, 0, 0), (0, 0, 1.4)], cell=cell) -atoms.center() -systems.append((atoms, 'Hydrogen molecule')) +def get_systems(): + cell = (5, 5, 5) + atoms = Atoms('H2', [(0, 0, 0), (0, 0, 1.4)], cell=cell) + atoms.center() + systems.append((atoms, 'Hydrogen molecule')) -# -atoms = FaceCenteredCubic( - directions=[[1, -1, 0], [1, 1, 0], [0, 0, 1]], - size=(2, 2, 2), - symbol='Cu', - pbc=(1, 1, 1)) -atoms.rattle(stdev=0.1, seed=42) -systems.append((atoms, 'Shaken bulk copper')) + atoms = FaceCenteredCubic( + directions=[[1, -1, 0], [1, 1, 0], [0, 0, 1]], + size=(2, 2, 2), + symbol='Cu', + pbc=(1, 1, 1)) + atoms.rattle(stdev=0.1, seed=42) + systems.append((atoms, 'Shaken bulk copper')) -# -a = 2.70 -c = 1.59 * a + a = 2.70 + c = 1.59 * a -slab = Atoms('2Cu', [(0., 0., 0.), (1 / 3., 1 / 3., -0.5 * c)], - tags=(0, 1), - pbc=(1, 1, 0)) -slab.set_cell([(a, 0, 0), - (a / 2, 3**0.5 * a / 2, 0), - (0, 0, 1)]) -slab.center(vacuum=3, axis=2) -mask = [a.tag == 1 for a in slab] -slab.set_constraint(FixAtoms(mask=mask)) -systems.append((slab, 'Distorted Cu(111) surface')) + slab = Atoms('2Cu', [(0., 0., 0.), (1 / 3., 1 / 3., -0.5 * c)], + tags=(0, 1), + pbc=(1, 1, 0)) + slab.set_cell([(a, 0, 0), + (a / 2, 3**0.5 * a / 2, 0), + (0, 0, 1)]) + slab.center(vacuum=3, axis=2) + mask = [a.tag == 1 for a in slab] + slab.set_constraint(FixAtoms(mask=mask)) + systems.append((slab, 'Distorted Cu(111) surface')) -# -zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197 -xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19 -co = Atoms('CO', positions=[(-xpos + 1.2, 0, -zpos), - (-xpos + 1.2, -1.1, -zpos)]) -slab = fcc111('Au', size=(2, 2, 2), orthogonal=True) -add_adsorbate(slab, co, 1.5, 'bridge') -slab.center(vacuum=6, axis=2) -slab.set_pbc((True, True, False)) -constraint = FixAtoms(mask=[a.tag == 2 for a in slab]) -slab.set_constraint(constraint) -systems.append((slab, 'CO on Au(111) surface')) + zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197 + xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19 + co = Atoms('CO', positions=[(-xpos + 1.2, 0, -zpos), + (-xpos + 1.2, -1.1, -zpos)]) + slab = fcc111('Au', size=(2, 2, 2), orthogonal=True) + add_adsorbate(slab, co, 1.5, 'bridge') + slab.center(vacuum=6, axis=2) + slab.set_pbc((True, True, False)) + constraint = FixAtoms(mask=[a.tag == 2 for a in slab]) + slab.set_constraint(constraint) + systems.append((slab, 'CO on Au(111) surface')) -# -atoms = Atoms(symbols='C5H12', - cell=[16.83752497, 12.18645905, 11.83462179], - positions=[[5.90380523, 5.65545388, 5.91569796], - [7.15617518, 6.52907738, 5.91569796], - [8.41815022, 5.66384716, 5.92196554], - [9.68108996, 6.52891016, 5.91022362], - [10.93006206, 5.65545388, 5.91569796], - [5.00000011, 6.30002353, 5.9163716], - [5.88571848, 5.0122839, 6.82246859], - [5.88625613, 5.01308931, 5.01214155], - [7.14329342, 7.18115393, 6.81640316], - [7.14551332, 7.17200869, 5.00879027], - [8.41609966, 5.00661165, 5.02355167], - [8.41971183, 5.0251482, 6.83462168], - [9.69568096, 7.18645894, 6.8078633], - [9.68914668, 7.16663649, 5.00000011], - [10.95518898, 5.02163182, 6.8289018], - [11.83752486, 6.29836826, 5.90274952], - [10.94464142, 5.00000011, 5.01802495]]) -systems.append((atoms, 'Pentane molecule')) + atoms = Atoms(symbols='C5H12', + cell=[16.83752497, 12.18645905, 11.83462179], + positions=[[5.90380523, 5.65545388, 5.91569796], + [7.15617518, 6.52907738, 5.91569796], + [8.41815022, 5.66384716, 5.92196554], + [9.68108996, 6.52891016, 5.91022362], + [10.93006206, 5.65545388, 5.91569796], + [5.00000011, 6.30002353, 5.9163716], + [5.88571848, 5.0122839, 6.82246859], + [5.88625613, 5.01308931, 5.01214155], + [7.14329342, 7.18115393, 6.81640316], + [7.14551332, 7.17200869, 5.00879027], + [8.41609966, 5.00661165, 5.02355167], + [8.41971183, 5.0251482, 6.83462168], + [9.69568096, 7.18645894, 6.8078633], + [9.68914668, 7.16663649, 5.00000011], + [10.95518898, 5.02163182, 6.8289018], + [11.83752486, 6.29836826, 5.90274952], + [10.94464142, 5.00000011, 5.01802495]]) + systems.append((atoms, 'Pentane molecule')) -# -slab = fcc100('Cu', size=(2, 2, 2), vacuum=3.5) -add_adsorbate(slab, 'C', 1.5, 'hollow') -mask = [a.tag > 1 for a in slab] -constraint = FixAtoms(mask=mask) -slab.set_constraint(constraint) -systems.append((slab, 'C/Cu(100)')) - -# -surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)] -esurf = [0.9151, 0.9771, 0.7953] # Surface energies -size = 10 # number of atoms -atoms = wulff_construction('Al', surfaces, esurf, size, 'fcc', - rounding='above') -atoms.center(vacuum=6) -atoms.rattle(0.2) -systems.append((atoms, 'Alumninum cluster')) + slab = fcc100('Cu', size=(2, 2, 2), vacuum=3.5) + add_adsorbate(slab, 'C', 1.5, 'hollow') + mask = [a.tag > 1 for a in slab] + constraint = FixAtoms(mask=mask) + slab.set_constraint(constraint) + systems.append((slab, 'C/Cu(100)')) + surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)] + esurf = [0.9151, 0.9771, 0.7953] # Surface energies + size = 10 # number of atoms + atoms = wulff_construction('Al', surfaces, esurf, size, 'fcc', + rounding='above') + atoms.center(vacuum=6) + atoms.rattle(0.2) + systems.append((atoms, 'Alumninum cluster')) + return systems def create_database(): + systems = get_systems() db = connect('systems.db', append=False) for atoms, description in systems: name = atoms.get_chemical_formula() -- GitLab From c0d155a34dd4115c0aa1c16bb218d808ddfcbbeb Mon Sep 17 00:00:00 2001 From: Ask Hjorth Larsen Date: Fri, 4 Feb 2022 14:36:13 +0100 Subject: [PATCH 2/4] update warning handling to appease old and new pytest simultaneously --- ase/test/test_imports.py | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/ase/test/test_imports.py b/ase/test/test_imports.py index 5267a0695..93c3bfa91 100644 --- a/ase/test/test_imports.py +++ b/ase/test/test_imports.py @@ -1,3 +1,4 @@ +import contextlib from pathlib import Path from importlib import import_module from numpy import VisibleDeprecationWarning @@ -58,17 +59,18 @@ newpy_only_modules = { @pytest.mark.filterwarnings('ignore:Moved to') def test_imports(): for module in all_modules: - if module in deprecated_modules: - warning = (DeprecationWarning, VisibleDeprecationWarning) - else: - warning = None + with contextlib.ExitStack() as ignored_warnings: + if module in deprecated_modules: + ignored_warnings.enter_context( + pytest.warns((DeprecationWarning, + VisibleDeprecationWarning))) - try: - with pytest.warns(warning): + try: import_module(module) - except SyntaxError: - if module not in newpy_only_modules: - raise - except ImportError as err: - if err.name not in ignore_imports and 'deprecated' not in str(err): - raise + except SyntaxError: + if module not in newpy_only_modules: + raise + except ImportError as err: + ok = err.name in ignore_imports or 'deprecated' in str(err) + if not ok: + raise -- GitLab From 74dba1a8cfe4ee79c1436bdcf0195b79e7c5536e Mon Sep 17 00:00:00 2001 From: Ask Hjorth Larsen Date: Fri, 4 Feb 2022 14:41:38 +0100 Subject: [PATCH 3/4] update pytest.warns() call to latest pytest --- ase/test/calculator/castep/test_castep_interface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ase/test/calculator/castep/test_castep_interface.py b/ase/test/calculator/castep/test_castep_interface.py index 623836b62..08c72c65d 100644 --- a/ase/test/calculator/castep/test_castep_interface.py +++ b/ase/test/calculator/castep/test_castep_interface.py @@ -121,7 +121,7 @@ def test_fundamental_params(): # Test special parsers mock_cparam.continuation = 'default' - with pytest.warns(None): + with pytest.warns(UserWarning): mock_cparam.reuse = 'default' assert mock_cparam.reuse.value is None -- GitLab From ac18ea7145eace58aabe4047b6214faf6cf5703f Mon Sep 17 00:00:00 2001 From: Ask Hjorth Larsen Date: Fri, 4 Feb 2022 15:00:43 +0100 Subject: [PATCH 4/4] oops, fix undefined variable --- ase/optimize/test/systems.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ase/optimize/test/systems.py b/ase/optimize/test/systems.py index 3014efe37..9769eaf61 100644 --- a/ase/optimize/test/systems.py +++ b/ase/optimize/test/systems.py @@ -9,6 +9,8 @@ from ase.cluster import wulff_construction def get_systems(): + systems = [] + cell = (5, 5, 5) atoms = Atoms('H2', [(0, 0, 0), (0, 0, 1.4)], cell=cell) atoms.center() @@ -86,6 +88,7 @@ def get_systems(): systems.append((atoms, 'Alumninum cluster')) return systems + def create_database(): systems = get_systems() db = connect('systems.db', append=False) -- GitLab