4.2.2rc #4751
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4.2.2rc #4751
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Fixes espressomd#4735 Description of changes: - fix the URL in the GitHub CI report (new GitLab routing system)
Description of changes: - bugfix: inertialess tracers are now integrated along the z-axis (regression introduced in February 2022) - bugfix: a runtime exception is now raised when using more than 1 MPI rank with inertialess tracers + LB GPU - with LB GPU, inertialess tracers are silently skipped on MPI ranks >= 2
Description of changes: - fix compiler diagnostics from Clang 16.0.0 and GCC 13.0 - reduce the amount of `-Wconversion` diagnostics
Description of changes: - silence non-critical deprecation warning in Cython-generated code when building in C++20 mode
Description of changes: - fix import errors in several tests, tutorials and benchmarks due to API changes in setuptools >= 67.3.0
Fixes espressomd#4719 Description of changes: - extract the correct particle radius from the interaction list
…4724) Fixes espressomd#4280 Description of changes: - checkpoint restrictions on the number of MPI ranks have been lifted
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Follow up to our work with HPC Vega and the EESSI project. Description of changes: - add GPU support in P3M and LB - remove MASS dependency in P3M - adjust steepest descent for large particle numbers
Description of changes: - Resizing the box now throws a runtime error if there are constraints present, since constraint preconditions might no longer be fulfilled (e.g. a wall constraint might end up outside the box boundaries when the box shrinks) - This feature was originally introduced in ESPResSo 4.0.0 (espressomd#2031), but never actually worked because the PR accidentally removed the event function call during merge conflict resolution
Fixes espressomd#4787 Description of changes: - the energy and pressure observables now correctly tally non-bonded contributions
Description of changes: - add missing FFTW3 MPI library dependency - pin Jupyter Notebook package versions (follow-up to espressomd#4789 (comment))
Description of changes: - bugfix: `OifCell.elastic_forces()` no longer throws a `TypeError` - add a smoke test for that function
…spressomd#4827) Fixes espressomd#4825 Description of changes: * Bugfix: particles outside the simulation box are now properly coupled using PBC. The coordinates are folded before considering shifted positions in the LB particle coupling code. Also, a test that fails without the fix is added. To my understanding, if the particle position is folded, and then all combination of `folded_pos[i]` +/- `box_l[i]` for all Cartesian directions are considered, both the particle in the primary box and all potential halo regions are caught.
Fixes espressomd#4838 Description of changes: - fix virtual sites regression introduced in ESPResSo 4.2.0 - update description of `MASS` and `ROTATIONAL_INERTIA` features
Fixes espressomd#4842 Description of changes: - The current implementation of 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.
Starting with Python 3.12, package `unittest` returns exit code 5 when all tests are skipped. By default, CTest treats any non-zero exit code as a failure. This can be remediated by setting test property [`SKIP_RETURN_CODE`](https://cmake.org/cmake/help/latest/prop_test/SKIP_RETURN_CODE.html) to 5. Description of changes: - skipped tests are no longer treated as failures by CTest
Fixes espressomd#4856 Description of changes: - fix multiple bugs caused by undefined behavior due to the static initialization order of MPI global objects - ESPResSo is now compatible with Boost 1.84+
Due to a recent update in Ubuntu 20.04 and 22.04, ASAN no longer works in a MPI environment.
…d#4898) Fixes espressomd#4897 Description of changes: - fix issues in the description of observable return values and array shapes - fix vector notation in the expressions of single-particle force constraints - make notation more consistent across particle-based observables
Fixes espressomd#4834 Description of changes: - 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; use `system.change_volume_and_rescale_particles()` instead, which properly rescales particle positions.
Modern CUDA releases use 256 characters.
Release 4.2.0 generalized the use of utility functions to convert Python vector-valued objects of size 3 to the corresponding C++ script interface Vector3d or Vector3i types. Exceptions raised in these functions were not propagated to the Python interpreter, printing "Exception ignored in: 'espressomd.utils.make_Vector3d'" to the screen and leaving the call site with a fully or partially uninitialized object. This is now resolved.
Description of changes: - encourage the use of Python environments (venv, conda, etc.) in the installation instructions
Description of changes: - replace `np.product()` (deprecated in NumPy 1.15 and removed in NumPy 2.0) by `np.prod()` - bump Python version requirement of `requests` due to CVE-2024-35195 - adjust Python version requirements to resolve all dependency issues - `python3 -m pip install -r requirements.txt` now works again
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4.2.2 bugfix release.