File ase-mr3400-numpy2.patch of Package python-ase

Overview Repositories Revisions Requests Users Attributes Meta

File ase-mr3400-numpy2.patch of Package python-ase (Revision b908e56b462968e47d94eecfb16936a3)

Currently displaying revision b908e56b462968e47d94eecfb16936a3 , Show latest

From 06c59143e7fdf15483491cf71800afba8b862bda Mon Sep 17 00:00:00 2001
From: yuzie007 <yuji.ikeda.ac.jp@gmail.com>
Date: Thu, 20 Jun 2024 17:44:31 +0200
Subject: [PATCH 1/7] Use `np.exceptions.ComplexWarning`

---
 ase/test/vibrations/test_vib.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

Index: ase-3.23.0/ase/test/vibrations/test_vib.py
===================================================================
--- ase-3.23.0.orig/ase/test/vibrations/test_vib.py
+++ ase-3.23.0/ase/test/vibrations/test_vib.py
@@ -6,6 +6,10 @@ import numpy as np
 import pytest
 from numpy.testing import (assert_array_almost_equal,
                            assert_array_equal)
+try:
+    from numpy.exceptions import ComplexWarning  # NumPy 2.0.0
+except ImportError:
+    from numpy import ComplexWarning
 
 import ase.io
 from ase import Atoms, units
@@ -438,14 +442,14 @@ def test_constrained_atoms(n2_data):
 
 
 def test_dos(n2_vibdata):
-    with pytest.warns(np.ComplexWarning):
+    with pytest.warns(ComplexWarning):
         dos = n2_vibdata.get_dos()
     assert_array_almost_equal(dos.get_energies(),
                               n2_vibdata.get_energies())
 
 
 def test_pdos(n2_vibdata):
-    with pytest.warns(np.ComplexWarning):
+    with pytest.warns(ComplexWarning):
         pdos = n2_vibdata.get_pdos()
     assert_array_almost_equal(pdos[0].get_energies(),
                               n2_vibdata.get_energies())
Index: ase-3.23.0/ase/constraints.py
===================================================================
--- ase-3.23.0.orig/ase/constraints.py
+++ ase-3.23.0/ase/constraints.py
@@ -1161,19 +1161,19 @@ class FixInternals(FixConstraint):
         # Projection
         hh = []
         for i, constraint in enumerate(self.constraints):
-            hh.append(aa[:, i] * np.row_stack(aa[:, i]))
+            hh.append(aa[:, i] * np.vstack(aa[:, i]))
 
-        txx = aa[:, self.n] * np.row_stack(aa[:, self.n])
-        tyy = aa[:, self.n + 1] * np.row_stack(aa[:, self.n + 1])
-        tzz = aa[:, self.n + 2] * np.row_stack(aa[:, self.n + 2])
-        rxx = aa[:, self.n + 3] * np.row_stack(aa[:, self.n + 3])
-        ryy = aa[:, self.n + 4] * np.row_stack(aa[:, self.n + 4])
-        rzz = aa[:, self.n + 5] * np.row_stack(aa[:, self.n + 5])
+        txx = aa[:, self.n] * np.vstack(aa[:, self.n])
+        tyy = aa[:, self.n + 1] * np.vstack(aa[:, self.n + 1])
+        tzz = aa[:, self.n + 2] * np.vstack(aa[:, self.n + 2])
+        rxx = aa[:, self.n + 3] * np.vstack(aa[:, self.n + 3])
+        ryy = aa[:, self.n + 4] * np.vstack(aa[:, self.n + 4])
+        rzz = aa[:, self.n + 5] * np.vstack(aa[:, self.n + 5])
         T = txx + tyy + tzz + rxx + ryy + rzz
         for vec in hh:
             T += vec
-        ff = np.dot(T, np.row_stack(ff))
-        forces[:, :] -= np.dot(T, np.row_stack(ff)).reshape(-1, 3)
+        ff = np.dot(T, np.vstack(ff))
+        forces[:, :] -= np.dot(T, np.vstack(ff)).reshape(-1, 3)
 
     def __repr__(self):
         constraints = [repr(constr) for constr in self.constraints]
Index: ase-3.23.0/ase/mep/autoneb.py
===================================================================
--- ase-3.23.0.orig/ase/mep/autoneb.py
+++ ase-3.23.0/ase/mep/autoneb.py
@@ -544,7 +544,7 @@ class AutoNEB:
             try:
                 energies.append(a.get_potential_energy())
             except RuntimeError:
-                energies.append(np.NaN)
+                energies.append(np.nan)
         return energies
 
     def get_energies_one_image(self, image):
@@ -553,7 +553,7 @@ class AutoNEB:
         try:
             energy = image.get_potential_energy()
         except RuntimeError:
-            energy = np.NaN
+            energy = np.nan
         return energy
 
     def get_highest_energy_index(self):
Index: ase-3.23.0/ase/dft/__init__.py
===================================================================
--- ase-3.23.0.orig/ase/dft/__init__.py
+++ ase-3.23.0/ase/dft/__init__.py
@@ -1,4 +1,8 @@
 import numpy as np
+try:
+    from numpy import trapezoid  # NumPy 2.0.0
+except ImportError:
+    from numpy import trapz as trapezoid
 
 from ase.dft.dos import DOS
 from ase.dft.kpoints import monkhorst_pack
@@ -19,9 +23,9 @@ def get_distribution_moment(x, y, order=
     y = np.asarray(y)
 
     if order == 0:
-        return np.trapz(y, x)
+        return trapezoid(y, x)
     elif isinstance(order, int):
-        return np.trapz(x**order * y, x) / np.trapz(y, x)
+        return trapezoid(x**order * y, x) / trapezoid(y, x)
     elif hasattr(order, '__iter__'):
         return [get_distribution_moment(x, y, n) for n in order]
     else:
Index: ase-3.23.0/ase/md/switch_langevin.py
===================================================================
--- ase-3.23.0.orig/ase/md/switch_langevin.py
+++ ase-3.23.0/ase/md/switch_langevin.py
@@ -1,6 +1,10 @@
 from typing import Any, List, Optional
 
 import numpy as np
+try:
+    from numpy import trapezoid  # NumPy 2.0.0
+except ImportError:
+    from numpy import trapz as trapezoid
 
 from ase import Atoms
 from ase.calculators.mixing import MixedCalculator
@@ -117,7 +121,7 @@ class SwitchLangevin(Langevin):
         lambdas = self.path_data[:, 1]
         U1 = self.path_data[:, 2]
         U2 = self.path_data[:, 3]
-        delta_F = np.trapz(U2 - U1, lambdas)
+        delta_F = trapezoid(U2 - U1, lambdas)
         return delta_F
 
 
Index: ase-3.23.0/ase/test/calculator/test_harmonic.py
===================================================================
--- ase-3.23.0.orig/ase/test/calculator/test_harmonic.py
+++ ase-3.23.0/ase/test/calculator/test_harmonic.py
@@ -1,6 +1,10 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_array_almost_equal
+try:
+    from numpy import trapezoid  # NumPy 2.0.0
+except ImportError:
+    from numpy import trapz as trapezoid
 
 from ase import Atoms
 from ase.calculators.calculator import CalculationFailed, CalculatorSetupError
@@ -266,7 +270,7 @@ def test_thermodynamic_integration():
                 e0, e1 = calc_linearCombi.get_energy_contributions(atoms)
                 ediffs[lamb].append(float(e1) - float(e0))
             ediffs[lamb] = np.mean(ediffs[lamb])
-    dA = np.trapz([ediffs[lamb] for lamb in lambs], x=lambs)  # anharm. corr.
+    dA = trapezoid([ediffs[lamb] for lamb in lambs], x=lambs)  # anharm. corr.
     assert -0.005 < dA < 0.005  # the MD run is to short for convergence
     if dA == 0.0:
         raise ValueError('there is most likely something wrong, but it could '
Index: ase-3.23.0/ase/io/octopus/input.py
===================================================================
--- ase-3.23.0.orig/ase/io/octopus/input.py
+++ ase-3.23.0/ase/io/octopus/input.py
@@ -516,7 +516,7 @@ def atoms2kwargs(atoms, use_ase_cell):
 
         if atoms.cell.orthorhombic:
             Lsize = 0.5 * np.diag(cell)
-            kwargs['lsize'] = [[repr(size) for size in Lsize]]
+            kwargs['lsize'] = [[str(size) for size in Lsize]]
             # ASE uses (0...cell) while Octopus uses -L/2...L/2.
             # Lsize is really cell / 2, and we have to adjust our
             # positions by subtracting Lsize (see construction of the coords
@@ -533,7 +533,7 @@ def atoms2kwargs(atoms, use_ase_cell):
             if sym is None:
                 raise ValueError('Cannot represent atom X without tags and '
                                  'species info in atoms.info')
-        coord_block.append([repr(sym)] + [repr(x) for x in pos])
+        coord_block.append([repr(sym)] + [str(x) for x in pos])
 
     kwargs[coordtype] = coord_block
     npbc = sum(atoms.pbc)
Index: ase-3.23.0/ase/dft/band_structure.py
===================================================================
--- ase-3.23.0.orig/ase/dft/band_structure.py
+++ ase-3.23.0/ase/dft/band_structure.py
@@ -1,6 +1,9 @@
 import warnings
 
-from numpy import VisibleDeprecationWarning
+try:
+    from numpy.exceptions import VisibleDeprecationWarning  # NumPy 2.0.0
+except ImportError:
+    from numpy import VisibleDeprecationWarning
 
 from ase.spectrum.band_structure import *  # noqa: F401,F403
 
Index: ase-3.23.0/ase/test/test_imports.py
===================================================================
--- ase-3.23.0.orig/ase/test/test_imports.py
+++ ase-3.23.0/ase/test/test_imports.py
@@ -3,7 +3,10 @@ from importlib import import_module
 from pathlib import Path
 
 import pytest
-from numpy import VisibleDeprecationWarning
+try:
+    from numpy.exceptions import VisibleDeprecationWarning  # NumPy 2.0.0
+except ImportError:
+    from numpy import VisibleDeprecationWarning
 
 import ase

Places

File ase-mr3400-numpy2.patch of Package python-ase (Revision b908e56b462968e47d94eecfb16936a3)

Places