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| Name: python3-espressomd | Distribution: openSUSE Tumbleweed |
| Version: 4.2.2 | Vendor: openSUSE |
| Release: 2.2 | Build date: Wed Sep 11 21:01:36 2024 |
| Group: Unspecified | Build host: reproducible |
| Size: 11175491 | Source RPM: python3-espressomd-4.2.2-2.2.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: http://espressomd.org | |
| Summary: Parallel simulation software for soft matter research | |
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.
GPL-3.0-or-later
* Wed Sep 11 2024 Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Fix numpy.patch
* Wed Sep 11 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 2024 Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Exclude 32bit architectures
* Wed May 22 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 02 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 02 2023 Ondřej Súkup <mimi.vx@gmail.com>
- cleanup spec
- skip mpiio test
* Wed Apr 26 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 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 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 2022 Guillaume GARDET <guillaume.gardet@opensuse.org>
- Add upstream patch to fix test on aarch64:
* fix-broken-fft-check.patch
* Tue Jul 19 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 2022 Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- added rpath.patch to fix the failing Rpath checks (see
boo#1198352)
* Sat Apr 16 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 2021 Christoph Junghans <junghans@votca.org>
- added missing_size_t.patch, to workaround missing size_t (see
gh#espressomd/espresso#4274)
* Tue May 11 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).
/usr/bin/pypresso /usr/lib64/python3.11/site-packages/espressomd /usr/lib64/python3.11/site-packages/espressomd/Espresso_config.so /usr/lib64/python3.11/site-packages/espressomd/Espresso_core.so /usr/lib64/python3.11/site-packages/espressomd/Espresso_script_interface.so /usr/lib64/python3.11/site-packages/espressomd/Espresso_shapes.so /usr/lib64/python3.11/site-packages/espressomd/MDA_ESP /usr/lib64/python3.11/site-packages/espressomd/MDA_ESP/__init__.py /usr/lib64/python3.11/site-packages/espressomd/__cinit__.py /usr/lib64/python3.11/site-packages/espressomd/__init__.py /usr/lib64/python3.11/site-packages/espressomd/_init.so /usr/lib64/python3.11/site-packages/espressomd/accumulators.py /usr/lib64/python3.11/site-packages/espressomd/actors.py /usr/lib64/python3.11/site-packages/espressomd/analyze.so /usr/lib64/python3.11/site-packages/espressomd/bond_breakage.py /usr/lib64/python3.11/site-packages/espressomd/cell_system.py /usr/lib64/python3.11/site-packages/espressomd/checkpointing.py /usr/lib64/python3.11/site-packages/espressomd/cluster_analysis.py /usr/lib64/python3.11/site-packages/espressomd/code_info.so /usr/lib64/python3.11/site-packages/espressomd/collision_detection.py /usr/lib64/python3.11/site-packages/espressomd/comfixed.py /usr/lib64/python3.11/site-packages/espressomd/constraints.py /usr/lib64/python3.11/site-packages/espressomd/cuda_init.so /usr/lib64/python3.11/site-packages/espressomd/drude_helpers.py /usr/lib64/python3.11/site-packages/espressomd/ekboundaries.py /usr/lib64/python3.11/site-packages/espressomd/electrokinetics.so /usr/lib64/python3.11/site-packages/espressomd/electrostatic_extensions.py /usr/lib64/python3.11/site-packages/espressomd/electrostatics.py /usr/lib64/python3.11/site-packages/espressomd/galilei.so /usr/lib64/python3.11/site-packages/espressomd/gen_code_info.py /usr/lib64/python3.11/site-packages/espressomd/gen_pxiconfig.py /usr/lib64/python3.11/site-packages/espressomd/highlander.py /usr/lib64/python3.11/site-packages/espressomd/integrate.so /usr/lib64/python3.11/site-packages/espressomd/interactions.so /usr/lib64/python3.11/site-packages/espressomd/io /usr/lib64/python3.11/site-packages/espressomd/io/__init__.py /usr/lib64/python3.11/site-packages/espressomd/io/mpiio.py /usr/lib64/python3.11/site-packages/espressomd/io/writer /usr/lib64/python3.11/site-packages/espressomd/io/writer/__init__.py /usr/lib64/python3.11/site-packages/espressomd/io/writer/h5md.py /usr/lib64/python3.11/site-packages/espressomd/io/writer/vtf.py /usr/lib64/python3.11/site-packages/espressomd/lb.so /usr/lib64/python3.11/site-packages/espressomd/lbboundaries.py /usr/lib64/python3.11/site-packages/espressomd/lees_edwards.py /usr/lib64/python3.11/site-packages/espressomd/magnetostatics.py /usr/lib64/python3.11/site-packages/espressomd/math.py /usr/lib64/python3.11/site-packages/espressomd/observables.py /usr/lib64/python3.11/site-packages/espressomd/pair_criteria.py /usr/lib64/python3.11/site-packages/espressomd/particle_data.so /usr/lib64/python3.11/site-packages/espressomd/polymer.so /usr/lib64/python3.11/site-packages/espressomd/profiler.so /usr/lib64/python3.11/site-packages/espressomd/reaction_methods.py /usr/lib64/python3.11/site-packages/espressomd/rotation.py /usr/lib64/python3.11/site-packages/espressomd/script_interface.so /usr/lib64/python3.11/site-packages/espressomd/shapes.py /usr/lib64/python3.11/site-packages/espressomd/system.so /usr/lib64/python3.11/site-packages/espressomd/thermostat.so /usr/lib64/python3.11/site-packages/espressomd/utils.so /usr/lib64/python3.11/site-packages/espressomd/version.so /usr/lib64/python3.11/site-packages/espressomd/virtual_sites.py /usr/lib64/python3.11/site-packages/espressomd/visualization.py /usr/share/doc/packages/python3-espressomd /usr/share/doc/packages/python3-espressomd/AUTHORS /usr/share/doc/packages/python3-espressomd/ChangeLog /usr/share/doc/packages/python3-espressomd/NEWS /usr/share/doc/packages/python3-espressomd/Readme.md /usr/share/licenses/python3-espressomd /usr/share/licenses/python3-espressomd/COPYING
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