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- Add numpy.patch to improve NumPy 2.0 compatibility (gh#espressomd/espresso#4992)

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- Add cmake.patch to address CMake warnings (gh#espressomd/espresso#4992)

OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=55
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Jean-Noel Grad 2024-09-11 18:38:18 +00:00 committed by Git OBS Bridge
commit 1a0cd08b37
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## Default LFS
*.7z filter=lfs diff=lfs merge=lfs -text
*.bsp filter=lfs diff=lfs merge=lfs -text
*.bz2 filter=lfs diff=lfs merge=lfs -text
*.gem filter=lfs diff=lfs merge=lfs -text
*.gz filter=lfs diff=lfs merge=lfs -text
*.jar filter=lfs diff=lfs merge=lfs -text
*.lz filter=lfs diff=lfs merge=lfs -text
*.lzma filter=lfs diff=lfs merge=lfs -text
*.obscpio filter=lfs diff=lfs merge=lfs -text
*.oxt filter=lfs diff=lfs merge=lfs -text
*.pdf filter=lfs diff=lfs merge=lfs -text
*.png filter=lfs diff=lfs merge=lfs -text
*.rpm filter=lfs diff=lfs merge=lfs -text
*.tbz filter=lfs diff=lfs merge=lfs -text
*.tbz2 filter=lfs diff=lfs merge=lfs -text
*.tgz filter=lfs diff=lfs merge=lfs -text
*.ttf filter=lfs diff=lfs merge=lfs -text
*.txz filter=lfs diff=lfs merge=lfs -text
*.whl filter=lfs diff=lfs merge=lfs -text
*.xz filter=lfs diff=lfs merge=lfs -text
*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text

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.osc

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diff --git a/CMakeLists.txt b/CMakeLists.txt
index ac0432c34..bff6f289b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,7 +38,13 @@ if(POLICY CMP0148)
cmake_policy(SET CMP0148 OLD)
endif()
+if(POLICY CMP0167)
+ # use BoostConfig.cmake shipped with Boost 1.70+ instead of the one in CMake
+ cmake_policy(SET CMP0167 NEW)
+endif()
# CMake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+project(ESPResSo)
+
# C++ standard
enable_language(CXX)
@@ -49,5 +55,4 @@ set(CMAKE_CXX_EXTENSIONS OFF)
include(FeatureSummary)
include(GNUInstallDirs)
-project(ESPResSo)
include(option_enum)
if(POLICY CMP0074)
@@ -268,7 +273,5 @@ if(WITH_STOKESIAN_DYNAMICS)
set(STOKESIAN_DYNAMICS 1)
if(NOT stokesian_dynamics_POPULATED)
- FetchContent_Populate(stokesian_dynamics)
- add_subdirectory(${stokesian_dynamics_SOURCE_DIR}
- ${stokesian_dynamics_BINARY_DIR})
+ FetchContent_MakeAvailable(stokesian_dynamics)
endif()
endif(WITH_STOKESIAN_DYNAMICS)

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version https://git-lfs.github.com/spec/v1
oid sha256:2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76
size 13463564

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

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-------------------------------------------------------------------
Wed Sep 11 18:36:23 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Add numpy.patch to improve NumPy 2.0 compatibility (gh#espressomd/espresso#4992)
- Add cmake.patch to address CMake warnings (gh#espressomd/espresso#4992)
-------------------------------------------------------------------
Wed May 22 16:08:22 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Exclude 32bit architectures
-------------------------------------------------------------------
Wed May 22 14:36:04 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Update to 4.2.2:
This release provides a number of corrections for the ESPResSo 4.2 line.
We recommend that this release be used for all production simulations.
The interface has not been changed between ESPResSo 4.2.1 and 4.2.2.
However, some bugs were discovered which can affect simulation results.
Please find the list of changes below. The numbers in brackets refer to
ticket numbers on https://github.com/espressomd/espresso
Improved documentation
----------------------
* Installation instructions now mention the FFTW3 MPI dependency
of long-range solvers and provide recommended version numbers
for Jupyter Notebook dependencies (#4790).
* Installation instructions now mention Python environments (#4922).
* Observables not properly document return values, array shapes,
and use a more consistent mathematical notation (#4898).
Bug fixes
---------
* Fatal runtime errors due to MPI global variables lifetime
were addressed (#4858). Older ESPResSo releases built with
Boost 1.84 or later might randomly crash when exiting
the Python interpreter.
* Virtual sites no longer contribute to the kinetic energy
of the system (#4839). The regression was introduced
in April 2021 and affected the 4.2 branch of ESPResSo.
* Inertialess tracers are now integrated along the z-axis (#4714).
The regression was introduced in February 2022 and affected
the 4.2 branch of ESPResSo.
* Inertialess tracers now throw an exception when attempting to use
LB GPU with 2 or more MPI ranks (#4714). Before, tracers on non-root
MPI ranks would be silently ignored by the CUDA kernels,
and would have a constant velocity, either 0 if the particle never
visited the fluid domain on the root rank, or the last known velocity
if the particle was once on the root rank. This bug affected all
ESPResSo versions.
* Particles close to the faces of the simulation box are now properly
coupled to the LB fluid (#4827). Due to numerical instability, it was
previously possible for particles to be outside the box simulation by
a tiny amount and skip LB particle coupling. The probability of this
bug occurring was low, but could be enhanced in simulations that
purposefully placed particle near the faces of the simulation box:
polymers sheared by Lees-Edwards boundary conditions, raspberry
particles (colloids, bacteria, etc.) when crossing a periodic
boundary, or cell membranes placed close to a periodic boundary.
* Resizing the box now throws a runtime error if there are constraints
present (#4778), since constraint preconditions might no longer be
fulfilled. For example, a wall constraint might end up outside the
box boundaries when the box shrinks.
* Resizing the box via `system.box_l = new_box_l` now throws
a runtime error if there are particles present, because particle
position folding cannot be guaranteed to be correct (#4901);
use `system.change_volume_and_rescale_particles()` instead,
which properly rescales particle positions.
* The velocity Verlet NpT propagator doesn't apply friction and noise
on angular velocities. ESPResSo now throws an error when NpT
encounters a rotating particle (#4843). This bug affected all
ESPResSo versions.
* The Brownian thermostat can no longer be configured with
`act_on_virtual=True` due to an unresolved bug (#4295)
that will be addressed in the next minor release.
* Restrictions on the number of MPI ranks have been lifted from the
checkpointing mechanism (#4724). It is now possible to use
checkpointing again in MPI-parallel simulations when the system
contains LB boundaries or `Union` shape-based constraints.
These restrictions had been introduced in 4.2.0 for technical
reasons that have since been resolved.
* When passing an invalid value to a function that expects an input
parameter of type `list` of size 3, an exception is now raised (#4911).
Previously, some functions would print an error message and continue
their execution with uninitialized data.
* The per-`type` and per-`mol_id` contributions from
`system.analysis.energy()`, `system.analysis.pressure()`
and `system.analysis.pressure_tensor()` now return the correct
values (#4788). Older version of ESPResSo were confusing the
particle `mol_id` with the particle `type`. The total pressure
was unreliable when `mol_id` properties were set to non-zero values.
* The OpenGL visualizer now extracts the correct non-bonded potential
parameter `sigma` when feature `WCA` is compiled in but `LENNARD_JONES`
isn't (#4720). The regression was introduced in 4.2.1.
* Method `OifCell.elastic_forces()` no longer throws a `TypeError` (#4813).
* Benchmark scripts were adjusted to support large particle numbers (#4753).
Under the hood changes
----------------------
* Several Clang 16 and GCC 13 compiler diagnostics have been addressed
(#4715).
* A non-critical GCC C++20 deprecation warning in Cython-generated code
was disabled (#4725).
* Several deprecation warnings emitted by CMake 3.27 have been silenced
(#4792).
* Add support for setuptools version 67.3.0 and above (#4709).
* Add support for Python 3.12 in testsuites run by CTest (#4852).
* Python requirements have been updated (#4924).
* CI pipeline URLs have been fixed (#4736).
- Removed upstreamed patches:
- array-bounds.patch
- mpi.patch
- setuptools.patch
- tracers.patch
-------------------------------------------------------------------
Fri Feb 2 16:23:08 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Fix undefined behavior due to improper handling of MPI static globals
- Add mpi.patch to remove MPI globals (gh#espressomd/espresso#4858)
-------------------------------------------------------------------
Mon Oct 2 12:11:53 UTC 2023 - Ondřej Súkup <mimi.vx@gmail.com>
- cleanup spec
- skip mpiio test
-------------------------------------------------------------------
Wed Apr 26 18:06:17 UTC 2023 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Fix LB inertialess tracers bug, fix compiler warnings
- Add tracers.patch to fix LB inertialess tracers (gh#espressomd/espresso#4714)
- Add array-bounds.patch to fix compiler warnings (gh#espressomd/espresso#4715)
-------------------------------------------------------------------
Tue Apr 18 10:43:03 UTC 2023 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Update to 4.2.1:
This release provides a number of corrections for the ESPResSo
4.2 line. We recommend that this release be used for all
production simulations. The interface has not been changed
between ESPResSo 4.2.0 and 4.2.1. However, some bugs were
discovered which can affect simulation results. No further bug
fix releases will be provided for the 4.2 line.
Added functionality
-------------------
* P3M and DipolarP3M can now be used with the hybrid
decomposition cell system with 1 MPI rank (#4678).
* Lattice-Boltzmann can now be used with the N-square and
hybrid decomposition cell systems with 2 or more MPI ranks
(#4676).
Changed requirements
--------------------
* The nbconvert version requirement was bumped to 6.5.1 to
patch an XSS vulnerability (#4658).
Improved documentation
----------------------
* The user guide now documents how to improve the
reproducibility of simulations that have checkpointing
enabled (#4677).
* The user guide now reflects that the lattice-Boltzmann
profile observables can be used in parallel (#4583).
* The active matter tutorial now uses an adequate engine
dipole for the swimmer particle (#4585).
* The error analysis tutorials have been improved (#4597).
* The tutorials can now be used in VS Code Jupyter (both the
desktop and web versions) and the mathematical formula are
now correctly displayed (#4531).
* All ESPResSo-specific CMake options are now documented in
the installation chapter of the user guide (#4608).
* Python package installation instructions no longer feature
package version numbers; instead, `requirements.txt` is used
as a constraint file (#4638).
* MMM1D algorithms now properly document their parameter names
(#4677).
* Reaction methods now cite the relevant literature (#4681).
* Caveats for chain analysis methods are now documented
(#4698).
* Minor formatting issues in Sphinx and typos in Python
docstrings were addressed (#4608).
Interface changes
-----------------
* A new boolean property
`System.virtual_sites.override_cutoff_check` was introduced
to allow disabling the cutoff range checks from virtual
sites (#4623).
Removed functionality
---------------------
* The unused and untested `Analysis.v_kappa()` method was
removed (#4534).
Improved testing
----------------
* Improve unit testing of core functionality: P3M, MMM1D, OIF,
virtual sites, script interface factory (#4631).
Bug fixes
---------
* The checkpointing mechanism now properly restores the
particle quaternion and all derived quantities (#4637).
Release 4.2.0 introduced a regression that caused checkpoint
files to overwrite the particle quaternion/director by a
unit vector pointing along the z direction, when the
`DIPOLES` feature was part of the myconfig file. This lead
to incorrect trajectories when reloading a simulation from
a checkpoint file, if the particle director played a role in
the simulation (ex: relative virtual sites, Gay-Berne
potential, anisotropic particles, active particles, etc.).
In addition, the angular velocity in body frame was restored
with the wrong orientation. Since the default myconfig file
contains `DIPOLES`, most ESPResSo users were affected.
* The checkpointing mechanism now properly restores LB
boundaries (#4649). Release 4.2.0 introduced a regression
where reloading LB populations would accidentally reset LB
boundary flags.
* The checkpointing mechanism now restores P3M and DipolarP3M
solvers without triggering a re-tune (#4677). In previous
releases, the checkpointing code would automatically re-tune
these algorithms during a reload, causing tiny deviations in
the forces that were problematic for trajectory
reproducibility.
* Brownian dynamics now integrates the rotational dynamics of
rotatable particles whose position is fixed in 3D space
(#4548).
* Langevin dynamics now properly integrates particles with
anisotropic friction (#4683, #4690).
* A regression that caused virtual sites to incorrectly count
their image box when crossing a periodic boundary has been
fixed (#4564, #4707).
* Particles can no longer be created or updated with a
negative mass or a null mass (#4679).
* Particles created without a user-specified type can now
participate in reactions (#4589).
* When a Monte Carlo displacement move is rejected, the
original particle velocity is now restored (#4589).
* Reaction methods now raise an exception when accidentally
calling `method.reaction(steps=20)` instead of
`method.reaction(reaction_steps=20)` (#4666). Since 4.2.0
the `steps` argument was ignored, in which case the default
value `reaction_steps=1` would used by the core. Note that
in the next minor release of ESPResSo, the `reaction_steps`
argument will be renamed to `steps`.
* Reaction methods now rebuild the list of free particle ids
every time `WidomInsertion::calculate_particle_insertion_potential_energy()`
and `ReactionAlgorithm::do_reaction()` are called (#4609).
This was needed to allow multiple concurrent reactions, as
well as avoiding subtle bugs when both the user and a
reaction method tried to create a new particle with an id
that used to belong to a deleted particle.
* When all particles are cleared, the reaction methods type
map is now also cleared (#4645). In the past, it was
possible to attempt a reaction on particles that had just
been cleared from the system, which would raise an
exception. This bug affected all ESPResSo releases since
4.0.
* The `System.part.pairs()` method now returns the correct
particle pairs when particle ids aren't both contiguous and
starting from 0 (#4628). The regression was introduced in
release 4.2.0.
* The auto-exclusions feature no longer adds spurious
exclusions to particle ids in the range [1, distance]
(#4654). This bug would potentially break the physics of the
system and potentially raise an exception in a system with
non-contiguous particle ids. This regression was introduced
in release 2.2.0b.
* The structure factor analysis code no longer double-counts
particles when the same particle type is provided twice
(#4534).
* The minimal distance distribution analysis code no longer
has an arbitrary cutoff distance when the simulation box is
aperiodic (open boundaries); this would cause spurious
artifacts to appear in the histogram at
`r = np.sum(system.box_l)` when particles were further apart
than this arbitrary distance (#4534).
* The cluster analysis functions are now disabled for systems
with Lees-Edwards periodic boundaries, since the cluster
analysis position wrapping code doesn't properly handle the
shear offset (#4698).
* The chain analysis methods now raise an error when the
number of chains or beads per chain is invalid (#4708).
* The observable tests now longer rely on deprecated numpy
options that were removed in numpy 1.24 (#4635).
* The visualizer `*_arrows_type_materials` options now have an
effect on arrow materials (#4686).
* The visualizer exception handling mechanism has been made
less brittle (#4686).
* The visualizer no longer raises exception when the optional
dependency `freeglut` isn't installed (#4691).
* The visualizer can randomly freeze when using collision
detection or bond breakage; a temporary workaround has been
introduced that fixes the issue for simulations that use
only 1 MPI rank (#4686).
* The `__dir__()` method of script interface objects no longer
raises an exception (#4674).
* Compilation and testsuite issues involving missing or
incorrect feature guards were addressed (#4562, #4648).
* The build system no longer silently ignores invalid external
feature definitions in `myconfig.hpp` and CMake files
(#4608). This issue would only affect feature developers,
as well as users of very old compilers, and would lead to
ESPResSo builds missing features.
Under the hood changes
----------------------
* The Clang 14 and AppleClang 14 compilers are now supported
(#4601).
* Several Clang 14 compiler diagnostics have been addressed
(#4606).
* Boost 1.81 and later versions are now supported (#4655).
* Compiler errors on non-x86 architectures were addressed
(#4538).
* Test tolerances were adjusted for non-x86 architectures
(#4708).
* The pypresso script now prints a warning when running with
MCA binding policy "numa" on NUMA architectures that are not
supported in singleton mode by Open MPI 4.x (#4607).
* The config file generator has been rewritten to properly
handle external features and compiler errors (#4608).
* Security hardening for GitHub Workflows (#4577, #4638) and
Codecov (#4600).
* Deployment of the user guide to GitHub Pages now relies on
cloud providers to fetch JavaScript dependencies (#4656).
- Removed upstreamed patches:
- fix-broken-fft-check.patch
- boost-1.74.patch
- numpy-1.24.patch
- rpath.patch
- missing_size_t.patch
- hdf5.patch
- setuptools.patch
-------------------------------------------------------------------
Thu Jan 26 19:46:39 UTC 2023 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- added numpy-1.24.patch to fix the testsuite (see
gh#espressomd/espresso#4635)
-------------------------------------------------------------------
Thu Sep 15 07:47:38 UTC 2022 - Guillaume GARDET <guillaume.gardet@opensuse.org>
- Add upstream patch to fix test on aarch64:
* fix-broken-fft-check.patch
-------------------------------------------------------------------
Tue Jul 19 19:40:59 UTC 2022 - Matej Cepl <mcepl@suse.com>
- Update to 4.2.0:
This is a feature release, i.e., new functionality is added
to ESPResSo. New thermostats, cell systems and boundary
conditions have been introduced to simulate systems with
Stokesian Dynamics, Brownian Dynamics, strongly inhomogeneous
particle sizes or translation-invariant shear flow. The
interface underwent (non-silent) changes, therefore scripts
will have to be slightly adapted. Most notably, particle
access by id and particle slices have a new syntax, and
electrostatic/magnetostatic layer correction and reaction
methods have a different setup. All errors are also now
emitted as Python exceptions and are recoverable with minimal
effort. An additional focus of this release is the
simplification of both the C++ core and the Python script
interface to facilitate future extensions of ESPResSo. The
testing of ESPResSo's functionality has been extended
considerably. We recommend that this release be used for all
production simulations. No further bug fix releases will be
provided for the 4.1 line, and not all fixes are present in
ESPResSo 4.1.4.
Added functionality
-------------------
* `P3MGPU` now supports energy and pressure calculation via
the CPU kernels (#4506).
* `ELC` now works with `P3MGPU` (#4506).
* The LB grid now supports slicing operations (#4195) and LB
slices are equality comparable (#4268).
* Lees-Edwards boundary conditions can be used for
particle-based simulations (#4457). Lattice-Boltzmann
support will be added in the 4.3.0 release.
* The non-bonded energy of a single particle can be calculated
(#4401).
* The list of close neighbors of a single particle can be
extracted (#4401).
* Brownian Dynamics simulations can be carried out with the
newly added Brownian integrator and Brownian thermostat
(#1842).
* Stokesian Dynamics simulations can be carried out with the
newly added Stokesian integrator and Stokesian thermostat
(#3790, #3987).
* Bonded interactions can now be automatically broken when the
bond length exceeds a critical value (#4456). This feature
can be combined with collision detection to model reversible
bonds (#4464).
* A new cell system `HybridDecomposition` was introduced to
speed up simulations with inhomogeneous particle interaction
ranges (#4373).
* Shapes can be merged into meta-shapes (#3493, #3538).
* The `HollowConicalFrustum` can now be sliced open, made
thick and rotated to model quarter pipes in any orientation
(#4179). The main application is in the construction of
complex microchannel geometries via `LBBoundaries`.
* A parametric weight function was added to the DPD
interaction (#3570).
* H5MD output files now support a unit system (#3751).
* H5MD output files now support custom specifications to
control which particle and box properties to write to disk
(#4480).
* The `H5md` class is now checkpointable and usable in an
interactive Python session (#3751).
* MDAnalysis integration now provides bond information
(#3801).
- Give up on building on 32bit architectures (gh#espressomd/espresso#4537).
- Fix rpath in provided libraries and shebang in pypresso.
-------------------------------------------------------------------
Sat Apr 16 00:24:21 UTC 2022 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- added rpath.patch to fix the failing Rpath checks (see
boo#1198352)
-------------------------------------------------------------------
Sat Apr 16 00:19:40 UTC 2022 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- added hdf5.patch to fix builds with H5MD (see
gh#espressomd/espresso#3543)
-------------------------------------------------------------------
Mon Jul 12 22:24:29 UTC 2021 - Christoph Junghans <junghans@votca.org>
- added missing_size_t.patch, to workaround missing size_t (see
gh#espressomd/espresso#4274)
-------------------------------------------------------------------
Tue May 11 09:29:24 UTC 2021 - Dominique Leuenberger <dimstar@opensuse.org>
- Use openmpi4 on 'non-sle based systems' (aka Tumbleweed) (can't
use unversioned openmpi, as hdf5-openmpi-devel would not exist).
-------------------------------------------------------------------
Thu Oct 29 15:42:42 UTC 2020 - Christoph Junghans <junghans@votca.org>
- added boost-1.74.patch to fix build with boost-1.74
(gh#espressomd/espresso#3864)
-------------------------------------------------------------------
Tue Oct 20 19:03:28 UTC 2020 - Christoph Junghans <junghans@votca.org>
- Update to 4.1.4, see
https://github.com/espressomd/espresso/blob/4.1.4/NEWS for
details
-------------------------------------------------------------------
Tue Sep 8 20:26:00 UTC 2020 - Christoph Junghans <junghans@votca.org>
- fix unversioned Obsoletes: statement
-------------------------------------------------------------------
Fri Aug 21 16:36:20 UTC 2020 - Christoph Junghans <junghans@votca.org>
- force the use of shared hdf5 by setting HDF5_USE_SHLIB
-------------------------------------------------------------------
Wed Jul 8 19:14:39 UTC 2020 - Christoph Junghans <junghans@votca.org>
- Update to 4.1.3, see
https://github.com/espressomd/espresso/blob/4.1.3/NEWS for
details
- drop 3427.patch - merged upstream
-------------------------------------------------------------------
Thu May 21 21:52:51 UTC 2020 - Christoph Junghans <junghans@votca.org>
- Require: the right hdf5 library
-------------------------------------------------------------------
Mon May 11 20:57:59 UTC 2020 - Christoph Junghans <junghans@votca.org>
- enable hdf5 support
- python3-numpy & python3-h5md are needed at runtime
-------------------------------------------------------------------
Tue Jan 21 13:26:55 UTC 2020 - Christoph Junghans <junghans@votca.org>
- add 3427.patch to fix tests on i586
-------------------------------------------------------------------
Wed Jan 15 23:35:14 CET 2020 - Matej Cepl <mcepl@suse.com>
- Update to 4.1.2:
- The interface has not been changed between ESPResSo 4.1.1 and
4.1.2.
- General corrections and improvements:
- Remove correlation between the rotational noise and
translational noise in the Langevin thermostat (#3355)
- Fix a bug that may cause the wrong temperature to be set by
the Langevin and DPD thermostats in the first time step
after the system was altered from the Python level, e.g.,
by changing particles or interactions (#3341)
- Fix a bug that caused the DPD thermostat to generate an
incorrect velocity distribution when used together with the
Langevin thermostat (#3352)
- Fix a bug in MMM2D and ELC with potential boundary
conditions, where one of the correction factors was
over-counted resulting in wrong energies (#3310)
- Fix a bug that caused the wrong bonds to be deleted when
removing particles from the system (#3356)
- Fix an ambiguity in `ParticleSlice`: the values in the
square brackets refer to particle ids, not array indices
(#3367). This means the ill-defined syntax
`system.part[0:-1]` is no longer valid. See the User Guide
section on Setting up particles for more information.
- Remove the mass prefactor in the `ComForce` observable and
use the correct Particle ids in the
`ParticleAngularVelocities` and `ParticleBodyVelocities`
observables (#3380)
- Fix a rounding error that caused debug builds of ESPResSo
running with multiple MPI threads to crash when a particle
was placed exactly on the boundary between two cells
(#3377)
- Fix `espressomd.has_features()` for the corner case where
the list of all compiled-in features is passed as argument,
returning ``False`` instead of ``True`` (#3318)
- Refactor the random number generator code (#3349)
- Documentation and tutorials corrections and improvements:
- Improve documentation of Monte Carlo methods (#3254, #3330)
- Build system and platform-related corrections and
improvements:
- List all Python dependencies in `requirements.txt` with the
supported version numbers (#3300). Please note that most of
them are optional.
- Add `MPIEXEC_PREFLAGS` and `MPIEXEC_POSTFLAGS` to the
command lines of parallel tests (#3221)
- Add the `-oversubscribe` flag to the command lines of
parallel tests running with OpenMPI v2.X to avoid exiting
early from a Python test configured without `MAX_NUM_PROC`
on a machine with a hyperthreaded CPU where OpenMPI is
configured such that the number of threads cannot exceed
the number of cores (#3335)
- Refactor the CI, maintainer, Doxygen and pypresso shell
scripts to make them more portable and support filepaths
containing whitespaces (#3326, #3373)
- Fix a nvcc compiler warning on the empty config (#3329)
- Improved testing:
- Add a test for ELC and MMM2D using analytic expressions of
the force and energy (#3331)
- Sped-up seven Python tests (#3319)
- Fix a test that broke on s390x architectures with Fedora 31
(#3312)
- Fix tests that broke on i586 architectures with OpenSUSE
Tumbleweed (#3327, #3358)
-------------------------------------------------------------------
Fri Nov 15 16:24:45 UTC 2019 - Christoph Junghans <junghans@votca.org>
- Version bump to 4.1.1
* Restore checkpointing mechanism for the steepest descent and NPT
integrators, LB and NPT thermostats (#3245)
* Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and
lower are no longer supported (#3236)
* Fix `Integrator.set_isotropic_npt()`: remove the silent conversion of
the incorrect input parameter `direction=[0,0,0]` to `[1,1,1]` in the
core; the function now throws an exception for fixed-volume boxes;
this change is unlikely to break pypresso scripts since not providing
a value to `direction` or providing `[1,1,1]` were the two standard
ways to set up a box with all directions allowed to rescale (#3253)
* Fix `Integrator.set_vv()`: this function failed to set the velocity
Verlet integrator if the NPT integrator was active; this is now
resolved (#3274)
* Fix the random segmentation fault triggered by the removal of a
particle with a bond or a virtual site relationship to another
particle (#3288)
* Fix `system.part.writevtk()`: the function now writes down all
particles when using `types="all"` (#3290)
* Disable the deprecated and broken ENGINE shear torque calculation
feature; the feature will be completely removed from the core in
the upcoming 4.2 release (#3277)
* Fix unit conversion for the LB fluid viscosity (#3287)
-------------------------------------------------------------------
Tue Apr 30 18:06:33 UTC 2019 - Christoph Junghans <junghans@votca.org>
- Version bump to 4.0.2
*Corrections for bugs that may harm simulation results:
* A sign error in tabulated interactions was corrected such that
the force equals the negative gradient of the potential.
(#2519,2520)
* The flow field of the CPU lattice-Boltzmann implementation was
deleted when aspects of the molecular dynamics cell grid were
changed; E.g., when interactions, the skin or the parallelization
setup were changed. ESPResSo now terminates with an error, when this
happens. To avoid this, please setup the CPU lattice-Boltzmann after
all other aspects of the system. The GPU LB is not affected in the
4.0 release, but was affected in the current development branch.
(#2728, #2736)
* Corrected the force acting on LB Boundaries for the case of
agrid and density not equal to 1 (#2624).
* Corrected the cutoff calculation for the soft sphere interaction. In
the previous implementation, the offset parameter was ignored.
(#2505)
* The "three point coupling" of particles to the lattice-Boltzmann
method has been removed. While it works in most environments, for
some compilers the calculation gives wrong values. This is likely
caused by undefined behavior. A corrected implementation is
available in ESPResSo's development branch. It cannot be safely
backported to 4.0.2, because the code has diverged too far. (#2516,
#2517) Users who did not explicitly activate this coupling via
couple="3pt" are not affected.
* The velocity of existing particles was changed when setting or
changing the simulation time step (#2480)
* Further changes:
* Fixed the electrokinetic Python interface (#2486)
* Correction to the installation instructions for mac (#2510)
* Corrected file permissions (#2470)
* Minor corrections and extensions to the test suite (#2477, #2552)
* Fixed a dead-lock in the dipolar Barnes Hutt method on the GPU for
recent NVIDIA cards such as RTX 2080 (#2719).
* Restored Mayavi visualizer's API-compatibility with OpenGL
visualizer (#2751)
-------------------------------------------------------------------
Fri Jan 25 16:28:37 UTC 2019 - Christoph Junghans <junghans@votca.org>
- Version bump to 4.0.1
* Many small bugfixes
- Drop 2255.patch, 2259.patch and 2265.patch - merged upstream
-------------------------------------------------------------------
Fri Sep 28 23:13:13 UTC 2018 - Christoph Junghans <junghans@votca.org>
- added change from request #639007
- rename package to python3-espressomd
- install COPYING for all packages
- change license to GPL-3.0-or-later
- added sonum define
-------------------------------------------------------------------
Fri Sep 7 15:36:54 UTC 2018 - junghans@votca.org
- Version bump to 4.0.0
- Rename pacakge to python-espressomd
- Dropped 1830.patch - merged upstream
- Dropped doc package - under rework in 4.0.0
- New features:
- Reaction ensemble methods for the modelling of chemical reactions, including constant pH and Wang-Landau schemes.
- Polarisable particles via the Drude-oscillator scheme.
- Steepest-descent energy minimization scheme.
- Methods for active particles (swimmer_reaction, dipolar swimmers).
- GPU-accelerated P3M method for electrostatic interactions.
- GPU-accelerated direct summation and Barnes-Hutt schemes for dipolar interactions under open boundary conditions.
- Support for the electrostatic and magnetostatics method provided by the ScaFaCoS library.
- Immersed boundary method for soft immersed objects in an LB fluid.
- Virtual sites acting as inertialess tracers in an LB fluid usable as part of the immersed boundary method or independently.
- New bonded quartic and Coulomb interactions.
- Possibility to tune the skin parameter.
- Support for saving to the h5md file format for molecular dynamics data.
- Connection to the MD Analysis Python package.
- A rotate_system command was added, which rotates the particle positions around the system’s center of mass.
- Added 2255.patch to fix numpy issue on i586
- Added 2259.patch to fix numpy issue on big-endian platforms
- Added 2265.patch to fix test on i586
-------------------------------------------------------------------
Mon Feb 12 19:25:01 UTC 2018 - junghans@votca.org
- add 1830.patch to fix install
- update version 3.3.1+git20180203.f74064d
* many many small fixes
* support for newer cython
-------------------------------------------------------------------
Wed Oct 25 12:43:08 UTC 2017 - junghans@votca.org
- adapt to new openlmi package - source mpivars.h during build
-------------------------------------------------------------------
Wed Feb 1 10:36:28 UTC 2017 - adam.majer@suse.de
- use individual libboost-*-devel packages instead of boost-devel
-------------------------------------------------------------------
Thu Sep 29 13:46:20 UTC 2016 - jengelh@inai.de
- RPM group fixup
-------------------------------------------------------------------
Wed Aug 3 17:54:16 UTC 2016 - junghans@votca.org
- switched to cmake build-system
- build python module
- dropped header as they are for internal use only
- dropped pkg-config files as nothing depends on libs yet
- update version 3.3.1+git20160803.6ed0518.tar.gz
* overhaul of buildsystem
* many many small fixes
-------------------------------------------------------------------
Sun Jun 26 07:35:00 UTC 2016 - i@marguerite.su
- fix boo#985147
* there's a commit that removed redefinition of malloc and realloc
which fixed build for gcc 6. but it's too hard to cherry pick, so
update to the latest git version is a good idea
- there's no --without-mpi option left in configure.ac, so "-openmpi"
sub-package is meaningless now (everything has openmpi support)
and since there's no two main packages any more, "-common" sub-package
is also meaningless now (and it doesn't contains data), merged.
- add sub-package: "-devel", "libEspresso0", "libEspressoTcl0"
- add generate_headers.rb to gather those .hpp that're really used
into "-devel" sub-package
- create pkgconfig files
- add some texlive BuildRequires to build pdf documentation.
- update version 3.3.1+git20160622.6aa229c:
* added edge statistics for meshes used by object-in-fluid
* added pos_folded property
* Adapted simple LB tests to current interface.
* system.part.writevtk()
* redesigned exclusions and added slice input
* Scafacos: Add long range energy to correct place in energy data structure
* Correction to scafacos energy calculation: Check cutoff in near field contrib
* Scafacos: Sort out conditional compilation and cython includes
* Scafacos: methods shared between electrostatics and dipolar calculations
-------------------------------------------------------------------
Sun Nov 8 21:57:37 UTC 2015 - p.drouand@gmail.com
- Update to version 3.3.1
* A lot of changes; please read the NEWS file
-------------------------------------------------------------------
Tue Aug 12 03:44:16 UTC 2014 - junghans@votca.org
- version bumped to 3.3.0
- Highlights of this release include:
- Calculation of the electrokinetic equations via the ELECTROKINETICS feature,
- the Shan/Chen method for multi component lattice Boltzmann fluids,
- the P3M and MMM1D methods can now be computed on a GPU,
- ESPResSo now has a rudimentary Python interface.
For a complete list of the changes in the release, please refer to:
http://download.savannah.gnu.org/releases/espressomd/NEWS
-------------------------------------------------------------------
Fri Feb 7 17:41:18 UTC 2014 - junghans@votca.org
- build openmpi and non-mpi version
-------------------------------------------------------------------
Tue Feb 4 18:59:10 UTC 2014 - junghans@votca.org
- initial commit

111
python3-espressomd.spec Normal file
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@ -0,0 +1,111 @@
#
# spec file for package python3-espressomd
#
# Copyright (c) 2024 SUSE LLC
# Copyright (c) 2014 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
# Build with OpenMPI
%define mpiver openmpi4
%define pkgname espresso
%define modname %{pkgname}md
Name: python3-%{modname}
Version: 4.2.2
Release: 0
Summary: Parallel simulation software for soft matter research
License: GPL-3.0-or-later
URL: http://espressomd.org
Source: https://github.com/%{modname}/%{pkgname}/releases/download/%{version}/%{pkgname}-%{version}.tar.gz
# PATCH-FIX-UPSTREAM numpy.patch gh#espressomd/espresso#4992
Patch0: numpy.patch
# PATCH-FIX-UPSTREAM cmake.patch gh#espressomd/espresso#4992
Patch1: cmake.patch
# According to gh#espressomd/espresso#4537 32bit architectures are not supported any more
ExcludeArch: %{ix86} armv7l
BuildRequires: cmake
BuildRequires: fftw3-devel
BuildRequires: gcc-c++
# Currently libboost_mpi-devel and hdf5 use different mpi versions
# BuildRequires: hdf5-devel
BuildRequires: %{mpiver}-devel
BuildRequires: chrpath
BuildRequires: gsl-devel
BuildRequires: hdf5-%{mpiver}-devel
BuildRequires: libboost_filesystem-devel
BuildRequires: libboost_mpi-devel
BuildRequires: libboost_system-devel
BuildRequires: libboost_test-devel
BuildRequires: python3-Cython < 3.0.10
BuildRequires: python3-devel
BuildRequires: python3-h5py
BuildRequires: python3-numpy-devel
BuildRequires: python3-scipy
BuildRequires: python3-setuptools
BuildRequires: zlib-devel
Provides: libEspresso4 = %{version}-%{release}
Obsoletes: libEspresso4 < 4.1
Requires: python3-h5py
Requires: python3-numpy
# make sure rpm pulls in the right dependency
Requires: libhdf5-%{mpiver}
%description
ESPResSo is a highly versatile software package for performing and analyzing
scientific Molecular Dynamics many-particle simulations of coarse-grained
atomistic or bead-spring models as they are used in soft-matter research in
physics, chemistry and molecular biology. It can be used to simulate systems
such as polymers, liquid crystals, colloids, ferrofluids and biological
systems, for example DNA and lipid membranes.
%prep
%autosetup -p1 -n %{pkgname}
# Fix shebang line for pypresso
sed -i -E '1s@^#!/usr/bin/env[[:blank:]]+sh@#!/bin/sh@' src/python/pypresso.cmakein
# skip mpiio test - it fails if inwoked with cmake, direct run with python3 -m unittest pass
sed -i '/mpiio\.py/d' testsuite/python/CMakeLists.txt
%build
source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh
# gh#espressomd/espresso#3396
%define _lto_cflags %{nil}
#force usage of shared hdf5
export HDF5_USE_SHLIB=yes
# overwrite .so linker flags on SUSE distros: drop --no-undefined
# we don't install {i,}pypresso scripts as they aren't needed when installing in /usr
%cmake \
-DCMAKE_SHARED_LINKER_FLAGS='-Wl,--as-needed -Wl,-z,now' \
-DCMAKE_SKIP_RPATH=ON \
-DLIBDIR=%{_libdir} \
-DPYTHON_EXECUTABLE=%{_bindir}/python3 \
-DPYTHON_INSTDIR=%{python3_sitearch} \
-DINSTALL_PYPRESSO=ON
%make_jobs
%install
%cmake_install
find %{buildroot}%{python3_sitearch} -name \*.so \
-exec chrpath -r %{python3_sitearch} '{}' \;
%check
LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}}
%files
%license COPYING
%doc Readme.md AUTHORS NEWS ChangeLog
%{_bindir}/pypresso
%{python3_sitearch}/espressomd
%changelog