File python3-espressomd.changes of Package python3-espressomd

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File python3-espressomd.changes of Package python3-espressomd (Revision d03ffdd282ce0377ffc956db9a7bec4b)

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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).

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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)

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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)

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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)

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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).

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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)

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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

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Tue Sep  8 20:26:00 UTC 2020 - Christoph Junghans <junghans@votca.org>

- fix unversioned Obsoletes: statement

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Fri Aug 21 16:36:20 UTC 2020 - Christoph Junghans <junghans@votca.org>

- force the use of shared hdf5 by setting HDF5_USE_SHLIB

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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

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Thu May 21 21:52:51 UTC 2020 - Christoph Junghans <junghans@votca.org>

- Require: the right hdf5 library

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Mon May 11 20:57:59 UTC 2020 - Christoph Junghans <junghans@votca.org>

- enable hdf5 support
- python3-numpy & python3-h5md are needed at runtime

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Tue Jan 21 13:26:55 UTC 2020 - Christoph Junghans <junghans@votca.org>

- add 3427.patch to fix tests on i586

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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)

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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)

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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)

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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

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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

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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

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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

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Wed Oct 25 12:43:08 UTC 2017 - junghans@votca.org

- adapt to new openlmi package - source mpivars.h during build

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Wed Feb  1 10:36:28 UTC 2017 - adam.majer@suse.de

- use individual libboost-*-devel packages instead of boost-devel

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Thu Sep 29 13:46:20 UTC 2016 - jengelh@inai.de

- RPM group fixup

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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

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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

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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

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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

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Fri Feb  7 17:41:18 UTC 2014 - junghans@votca.org

- build openmpi and non-mpi version

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Tue Feb  4 18:59:10 UTC 2014 - junghans@votca.org

- initial commit

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