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File python3-espressomd.changes of Package python3-espressomd
------------------------------------------------------------------- Wed Sep 11 19:01:36 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de> - Fix numpy.patch ------------------------------------------------------------------- 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
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