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boegelboegel
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Merge pull request #25153 from julianmorillo/ESPResSo
[foss/2025a] ESPResSo v4.2.2
2 parents 198ec8c + fb4595a commit 6c81c7e

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‎easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2025a.eb‎

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easyblock = 'CMakeMake'
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name = 'ESPResSo'
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version = '4.2.2'
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homepage = 'https://espressomd.org/wordpress'
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description = """A software package for performing and analyzing scientific Molecular Dynamics simulations."""
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source_urls = ['https://github.com/espressomd/espresso/releases/download/%(version)s/']
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sources = [SOURCELOWER_TAR_GZ]
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patches = ['ESPResSo-4.2.2_fix_unit_test_packaging_specifiers.patch',
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'ESPResSo-4.2.2_fix_numpy.patch']
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checksums = ['2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76',
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{'ESPResSo-4.2.2_fix_unit_test_packaging_specifiers.patch':
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'6fdb9a61812b7a1178804c82254e837bc69552cfc3d40011de3686ea1a6ff527'},
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{'ESPResSo-4.2.2_fix_numpy.patch':
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'1365be456d7d0c7c7243faee4a365a4d448e68ed1c044362a0b7be4d8c4b7dd7'},
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]
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toolchain = {'name': 'foss', 'version': '2025a'}
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toolchainopts = {'usempi': True, 'pic': True}
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builddependencies = [
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('CMake', '3.31.3'),
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('Cython', '3.1.1'),
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]
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dependencies = [
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('Python', '3.13.1'),
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('SciPy-bundle', '2025.06'),
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('Boost.MPI', '1.88.0'),
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('HDF5', '1.14.6'),
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('Mesa', '25.1.3'),
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('GSL', '2.8'),
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('IPython', '9.3.0'),
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('Pint', '0.24.4'),
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]
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configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF'
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# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!)
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configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python '
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runtest = 'check_unit_tests && make check_python'
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_binaries = ['ipypresso', 'pypresso']
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_libs = [
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'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes',
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'_init', 'analyze', 'code_info', 'electrokinetics', 'galilei',
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'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler',
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'script_interface', 'system', 'thermostat', 'utils', 'version',
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]
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_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
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sanity_check_paths = {
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'files': ['bin/%s' % x for x in _binaries] +
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[_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs],
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'dirs': ['bin', 'lib']
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}
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sanity_check_commands = ['pypresso -h', 'ipypresso -h']
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moduleclass = 'chem'

‎easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2_fix_numpy.patch‎

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# improve support for NumPy 2
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# https://github.com/espressomd/espresso/pull/4992
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# https://github.com/espressomd/espresso/pull/5034
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--- a/testsuite/python/thermostats_common.py
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+++ b/testsuite/python/thermostats_common.py
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@@ -19,2 +19,3 @@
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import numpy as np
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+import scipy.integrate
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@@ -28,3 +29,3 @@
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x = np.linspace(x1, x2, 1000)
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- return np.trapz(np.exp(-x**2 / (2. * kT)), x) / np.sqrt(2. * np.pi * kT)
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+ return scipy.integrate.trapezoid(np.exp(-x**2 / (2. * kT)), x=x) / np.sqrt(2. * np.pi * kT)
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--- a/testsuite/python/widom_insertion.py
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+++ b/testsuite/python/widom_insertion.py
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@@ -24,2 +24,3 @@
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import numpy as np
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+import scipy.integrate
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import espressomd
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@@ -52,3 +53,3 @@
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# coordinates
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- integrateUpToCutOff = 4 * np.pi * np.trapz(
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+ integrateUpToCutOff = 4 * np.pi * scipy.integrate.trapezoid(
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radius**2 * np.exp(-tests_common.lj_potential(radius,
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diff --git a/testsuite/python/brownian_dynamics.py b/testsuite/python/brownian_dynamics.py
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index 223340e15..f99d94018 100644
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--- a/testsuite/python/brownian_dynamics.py
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+++ b/testsuite/python/brownian_dynamics.py
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@@ -161,5 +161,5 @@ class BrownianThermostat(ut.TestCase):
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system.integrator.run(3)
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np.testing.assert_allclose(
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- part.omega_lab, [0, 0, 1.3 / 1.5], atol=1e-14)
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+ np.copy(part.omega_lab), [0, 0, 1.3 / 1.5], atol=1e-14)
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# noise only
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@@ -168,5 +168,5 @@ class BrownianThermostat(ut.TestCase):
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kT=1, gamma=1, gamma_rotation=1.5, act_on_virtual=False, seed=41)
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system.integrator.run(3)
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- self.assertGreater(np.linalg.norm(part.omega_lab), 0.)
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+ self.assertGreater(np.linalg.norm(np.copy(part.omega_lab)), 0.)
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diff --git a/testsuite/python/lees_edwards.py b/testsuite/python/lees_edwards.py
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index 002340bd2..4539f1af5 100644
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--- a/testsuite/python/lees_edwards.py
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+++ b/testsuite/python/lees_edwards.py
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@@ -397,5 +397,5 @@ class LeesEdwards(ut.TestCase):
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a=k_non_bonded / 2, n=-2, cutoff=r_cut)
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system.integrator.run(0)
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- r_12 = system.distance_vec(p1, p2)
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+ r_12 = np.copy(system.distance_vec(p1, p2))
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np.testing.assert_allclose(
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@@ -405,5 +405,5 @@ class LeesEdwards(ut.TestCase):
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np.testing.assert_allclose(
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np.copy(system.analysis.pressure_tensor()["non_bonded"]),
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- np.outer(r_12, p2.f) / system.volume())
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+ np.outer(r_12, np.copy(p2.f)) / system.volume())
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np.testing.assert_almost_equal(
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@@ -438,5 +438,5 @@ class LeesEdwards(ut.TestCase):
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shear_direction="x", shear_plane_normal="y", protocol=lin_protocol)
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# Test position and velocity of VS with Le shift
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- old_p3_pos = p3.pos
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+ old_p3_pos = np.copy(p3.pos)
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expected_p3_pos = old_p3_pos - \
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np.array((get_lin_pos_offset(system.time, **params_lin), 0, 0))
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@@ -444,5 +444,5 @@ class LeesEdwards(ut.TestCase):
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np.testing.assert_allclose(np.copy(p3.pos_folded), expected_p3_pos)
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np.testing.assert_allclose(
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- p3.v, p1.v + np.array((params_lin["shear_velocity"], 0, 0)))
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+ np.copy(p3.v), np.copy(p1.v) + np.array((params_lin["shear_velocity"], 0, 0)))
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# Check distances
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diff --git a/testsuite/python/test_checkpoint.py b/testsuite/python/test_checkpoint.py
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index f295cec44..4b30aaefb 100644
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--- a/testsuite/python/test_checkpoint.py
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+++ b/testsuite/python/test_checkpoint.py
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@@ -217,12 +217,12 @@ class CheckpointTest(ut.TestCase):
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np.testing.assert_allclose(np.copy(p3.ext_torque), [0.3, 0.5, 0.7])
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if espressomd.has_features('ROTATIONAL_INERTIA'):
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- np.testing.assert_allclose(p3.rinertia, [2., 3., 4.])
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+ np.testing.assert_allclose(np.copy(p3.rinertia), [2., 3., 4.])
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if espressomd.has_features('THERMOSTAT_PER_PARTICLE'):
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gamma = 2.
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if espressomd.has_features('PARTICLE_ANISOTROPY'):
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gamma = np.array([2., 3., 4.])
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- np.testing.assert_allclose(p4.gamma, gamma)
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+ np.testing.assert_allclose(np.copy(p4.gamma), gamma)
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if espressomd.has_features('ROTATION'):
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- np.testing.assert_allclose(p3.gamma_rot, 2. * gamma)
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+ np.testing.assert_allclose(np.copy(p3.gamma_rot), 2. * gamma)
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if espressomd.has_features('ENGINE'):
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self.assertEqual(p3.swimming, {"f_swim": 0.03, "mode": "N/A",
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@@ -237,9 +237,11 @@ class CheckpointTest(ut.TestCase):
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q_ind = ([1, 2, 3, 0],) # convert from scalar-first to scalar-last
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vs_id, vs_dist, vs_quat = p2.vs_relative
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- d = p2.pos - p1.pos
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+ d = np.copy(p2.pos - p1.pos)
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+ vs_quat = np.copy(vs_quat)
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+ p_quat = np.copy(p1.quat)
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theta = np.arccos(d[2] / np.linalg.norm(d))
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assert abs(theta - 3. * np.pi / 4.) < 1e-8
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q = np.array([0., 0., np.sin(theta / 2.), -np.cos(theta / 2.)])
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- r = R.from_quat(p1.quat[q_ind]) * R.from_quat(vs_quat[q_ind])
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+ r = R.from_quat(p_quat[q_ind]) * R.from_quat(vs_quat[q_ind])
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self.assertEqual(vs_id, p1.id)
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np.testing.assert_allclose(vs_dist, np.sqrt(2.))
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@@ -500,5 +502,5 @@ class CheckpointTest(ut.TestCase):
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self.assertEqual(p_virt.vs_relative[1], np.sqrt(2.))
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np.testing.assert_allclose(
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- p_real.vs_relative[2], [1., 0., 0., 0.], atol=1e-10)
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+ np.copy(p_real.vs_relative[2]), [1., 0., 0., 0.], atol=1e-10)
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def test_mean_variance_calculator(self):
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@@ -785,6 +787,6 @@ class CheckpointTest(ut.TestCase):
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p2 = system.part.add(pos=[system.box_l[0] - 1., 1.6, 0.], type=6)
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system.integrator.run(0, recalc_forces=True)
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- np.testing.assert_allclose(p1.f, [0., 1e8, 0.], atol=1e-3)
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- np.testing.assert_allclose(p2.f, [0., 1e8, 0.], atol=1e-3)
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+ np.testing.assert_allclose(np.copy(p1.f), [0., 1e8, 0.], atol=1e-3)
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+ np.testing.assert_allclose(np.copy(p2.f), [0., 1e8, 0.], atol=1e-3)
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p1.remove()
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p2.remove()

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