forked from pool/python-ase
Dirk Mueller
8c24dc3e4b
- Unpin numpy - Add ase-mr3400-numpy2.patch gl#ase/ase#3400 OBS-URL: https://build.opensuse.org/request/show/1197865 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-ase?expand=0&rev=9
223 lines
8.4 KiB
Diff
223 lines
8.4 KiB
Diff
From 06c59143e7fdf15483491cf71800afba8b862bda Mon Sep 17 00:00:00 2001
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From: yuzie007 <yuji.ikeda.ac.jp@gmail.com>
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Date: Thu, 20 Jun 2024 17:44:31 +0200
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Subject: [PATCH 1/7] Use `np.exceptions.ComplexWarning`
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---
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ase/test/vibrations/test_vib.py | 8 ++++++--
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1 file changed, 6 insertions(+), 2 deletions(-)
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Index: ase-3.23.0/ase/test/vibrations/test_vib.py
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===================================================================
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--- ase-3.23.0.orig/ase/test/vibrations/test_vib.py
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+++ ase-3.23.0/ase/test/vibrations/test_vib.py
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@@ -6,6 +6,10 @@ import numpy as np
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import pytest
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from numpy.testing import (assert_array_almost_equal,
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assert_array_equal)
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+try:
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+ from numpy.exceptions import ComplexWarning # NumPy 2.0.0
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+except ImportError:
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+ from numpy import ComplexWarning
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import ase.io
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from ase import Atoms, units
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@@ -438,14 +442,14 @@ def test_constrained_atoms(n2_data):
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def test_dos(n2_vibdata):
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- with pytest.warns(np.ComplexWarning):
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+ with pytest.warns(ComplexWarning):
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dos = n2_vibdata.get_dos()
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assert_array_almost_equal(dos.get_energies(),
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n2_vibdata.get_energies())
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def test_pdos(n2_vibdata):
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- with pytest.warns(np.ComplexWarning):
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+ with pytest.warns(ComplexWarning):
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pdos = n2_vibdata.get_pdos()
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assert_array_almost_equal(pdos[0].get_energies(),
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n2_vibdata.get_energies())
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Index: ase-3.23.0/ase/constraints.py
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===================================================================
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--- ase-3.23.0.orig/ase/constraints.py
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+++ ase-3.23.0/ase/constraints.py
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@@ -1161,19 +1161,19 @@ class FixInternals(FixConstraint):
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# Projection
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hh = []
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for i, constraint in enumerate(self.constraints):
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- hh.append(aa[:, i] * np.row_stack(aa[:, i]))
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+ hh.append(aa[:, i] * np.vstack(aa[:, i]))
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- txx = aa[:, self.n] * np.row_stack(aa[:, self.n])
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- tyy = aa[:, self.n + 1] * np.row_stack(aa[:, self.n + 1])
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- tzz = aa[:, self.n + 2] * np.row_stack(aa[:, self.n + 2])
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- rxx = aa[:, self.n + 3] * np.row_stack(aa[:, self.n + 3])
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- ryy = aa[:, self.n + 4] * np.row_stack(aa[:, self.n + 4])
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- rzz = aa[:, self.n + 5] * np.row_stack(aa[:, self.n + 5])
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+ txx = aa[:, self.n] * np.vstack(aa[:, self.n])
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+ tyy = aa[:, self.n + 1] * np.vstack(aa[:, self.n + 1])
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+ tzz = aa[:, self.n + 2] * np.vstack(aa[:, self.n + 2])
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+ rxx = aa[:, self.n + 3] * np.vstack(aa[:, self.n + 3])
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+ ryy = aa[:, self.n + 4] * np.vstack(aa[:, self.n + 4])
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+ rzz = aa[:, self.n + 5] * np.vstack(aa[:, self.n + 5])
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T = txx + tyy + tzz + rxx + ryy + rzz
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for vec in hh:
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T += vec
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- ff = np.dot(T, np.row_stack(ff))
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- forces[:, :] -= np.dot(T, np.row_stack(ff)).reshape(-1, 3)
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+ ff = np.dot(T, np.vstack(ff))
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+ forces[:, :] -= np.dot(T, np.vstack(ff)).reshape(-1, 3)
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def __repr__(self):
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constraints = [repr(constr) for constr in self.constraints]
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Index: ase-3.23.0/ase/mep/autoneb.py
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===================================================================
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--- ase-3.23.0.orig/ase/mep/autoneb.py
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+++ ase-3.23.0/ase/mep/autoneb.py
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@@ -544,7 +544,7 @@ class AutoNEB:
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try:
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energies.append(a.get_potential_energy())
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except RuntimeError:
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- energies.append(np.NaN)
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+ energies.append(np.nan)
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return energies
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def get_energies_one_image(self, image):
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@@ -553,7 +553,7 @@ class AutoNEB:
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try:
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energy = image.get_potential_energy()
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except RuntimeError:
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- energy = np.NaN
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+ energy = np.nan
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return energy
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def get_highest_energy_index(self):
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Index: ase-3.23.0/ase/dft/__init__.py
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===================================================================
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--- ase-3.23.0.orig/ase/dft/__init__.py
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+++ ase-3.23.0/ase/dft/__init__.py
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@@ -1,4 +1,8 @@
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import numpy as np
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+try:
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+ from numpy import trapezoid # NumPy 2.0.0
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+except ImportError:
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+ from numpy import trapz as trapezoid
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from ase.dft.dos import DOS
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from ase.dft.kpoints import monkhorst_pack
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@@ -19,9 +23,9 @@ def get_distribution_moment(x, y, order=
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y = np.asarray(y)
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if order == 0:
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- return np.trapz(y, x)
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+ return trapezoid(y, x)
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elif isinstance(order, int):
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- return np.trapz(x**order * y, x) / np.trapz(y, x)
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+ return trapezoid(x**order * y, x) / trapezoid(y, x)
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elif hasattr(order, '__iter__'):
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return [get_distribution_moment(x, y, n) for n in order]
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else:
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Index: ase-3.23.0/ase/md/switch_langevin.py
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===================================================================
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--- ase-3.23.0.orig/ase/md/switch_langevin.py
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+++ ase-3.23.0/ase/md/switch_langevin.py
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@@ -1,6 +1,10 @@
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from typing import Any, List, Optional
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import numpy as np
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+try:
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+ from numpy import trapezoid # NumPy 2.0.0
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+except ImportError:
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+ from numpy import trapz as trapezoid
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from ase import Atoms
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from ase.calculators.mixing import MixedCalculator
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@@ -117,7 +121,7 @@ class SwitchLangevin(Langevin):
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lambdas = self.path_data[:, 1]
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U1 = self.path_data[:, 2]
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U2 = self.path_data[:, 3]
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- delta_F = np.trapz(U2 - U1, lambdas)
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+ delta_F = trapezoid(U2 - U1, lambdas)
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return delta_F
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Index: ase-3.23.0/ase/test/calculator/test_harmonic.py
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===================================================================
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--- ase-3.23.0.orig/ase/test/calculator/test_harmonic.py
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+++ ase-3.23.0/ase/test/calculator/test_harmonic.py
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@@ -1,6 +1,10 @@
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import numpy as np
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import pytest
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from numpy.testing import assert_array_almost_equal
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+try:
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+ from numpy import trapezoid # NumPy 2.0.0
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+except ImportError:
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+ from numpy import trapz as trapezoid
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from ase import Atoms
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from ase.calculators.calculator import CalculationFailed, CalculatorSetupError
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@@ -266,7 +270,7 @@ def test_thermodynamic_integration():
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e0, e1 = calc_linearCombi.get_energy_contributions(atoms)
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ediffs[lamb].append(float(e1) - float(e0))
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ediffs[lamb] = np.mean(ediffs[lamb])
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- dA = np.trapz([ediffs[lamb] for lamb in lambs], x=lambs) # anharm. corr.
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+ dA = trapezoid([ediffs[lamb] for lamb in lambs], x=lambs) # anharm. corr.
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assert -0.005 < dA < 0.005 # the MD run is to short for convergence
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if dA == 0.0:
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raise ValueError('there is most likely something wrong, but it could '
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Index: ase-3.23.0/ase/io/octopus/input.py
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===================================================================
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--- ase-3.23.0.orig/ase/io/octopus/input.py
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+++ ase-3.23.0/ase/io/octopus/input.py
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@@ -516,7 +516,7 @@ def atoms2kwargs(atoms, use_ase_cell):
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if atoms.cell.orthorhombic:
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Lsize = 0.5 * np.diag(cell)
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- kwargs['lsize'] = [[repr(size) for size in Lsize]]
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+ kwargs['lsize'] = [[str(size) for size in Lsize]]
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# ASE uses (0...cell) while Octopus uses -L/2...L/2.
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# Lsize is really cell / 2, and we have to adjust our
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# positions by subtracting Lsize (see construction of the coords
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@@ -533,7 +533,7 @@ def atoms2kwargs(atoms, use_ase_cell):
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if sym is None:
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raise ValueError('Cannot represent atom X without tags and '
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'species info in atoms.info')
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- coord_block.append([repr(sym)] + [repr(x) for x in pos])
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+ coord_block.append([repr(sym)] + [str(x) for x in pos])
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kwargs[coordtype] = coord_block
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npbc = sum(atoms.pbc)
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Index: ase-3.23.0/ase/dft/band_structure.py
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===================================================================
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--- ase-3.23.0.orig/ase/dft/band_structure.py
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+++ ase-3.23.0/ase/dft/band_structure.py
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@@ -1,6 +1,9 @@
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import warnings
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-from numpy import VisibleDeprecationWarning
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+try:
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+ from numpy.exceptions import VisibleDeprecationWarning # NumPy 2.0.0
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+except ImportError:
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+ from numpy import VisibleDeprecationWarning
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from ase.spectrum.band_structure import * # noqa: F401,F403
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Index: ase-3.23.0/ase/test/test_imports.py
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===================================================================
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--- ase-3.23.0.orig/ase/test/test_imports.py
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+++ ase-3.23.0/ase/test/test_imports.py
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@@ -3,7 +3,10 @@ from importlib import import_module
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from pathlib import Path
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import pytest
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-from numpy import VisibleDeprecationWarning
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+try:
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+ from numpy.exceptions import VisibleDeprecationWarning # NumPy 2.0.0
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+except ImportError:
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+ from numpy import VisibleDeprecationWarning
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import ase
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