File python3-espressomd.changes of Package python3-espressomd

Overview Repositories Revisions Requests Users Attributes Meta

File python3-espressomd.changes of Package python3-espressomd (Revision 014c4b6637d4521c5e41b000e315e382)

Currently displaying revision 014c4b6637d4521c5e41b000e315e382 , Show latest

-------------------------------------------------------------------
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

Places

File python3-espressomd.changes of Package python3-espressomd (Revision 014c4b6637d4521c5e41b000e315e382)

Places