Index index by Group index by Distribution index by Vendor index by creation date index by Name Mirrors Help Search

python3-espressomd-4.2.0-1.1 RPM for ppc64le

From OpenSuSE Ports Tumbleweed for ppc64le

Name: python3-espressomd Distribution: openSUSE Tumbleweed
Version: 4.2.0 Vendor: openSUSE
Release: 1.1 Build date: Thu Jul 21 14:23:39 2022
Group: Productivity/Scientific/Chemistry Build host: obs-power9-10
Size: 14528468 Source RPM: python3-espressomd-4.2.0-1.1.src.rpm
Packager: http://bugs.opensuse.org
Url: http://espressomd.org
Summary: Parallel simulation software for soft matter research
ESPResSo is a highly versatile software package for performing and analyzing
scientific Molecular Dynamics many-particle simulations of coarse-grained
atomistic or bead-spring models as they are used in soft-matter research in
physics, chemistry and molecular biology. It can be used to simulate systems
such as polymers, liquid crystals, colloids, ferrofluids and biological
systems, for example DNA and lipid membranes.

Provides

Requires

License

GPL-3.0-or-later

Changelog

* Tue Jul 19 2022 Matej Cepl <mcepl@suse.com>
  - Update to 4.2.0:
      This is a feature release, i.e., new functionality is added
      to ESPResSo.  New thermostats, cell systems and boundary
      conditions have been introduced to simulate systems with
      Stokesian Dynamics, Brownian Dynamics, strongly inhomogeneous
      particle sizes or translation-invariant shear flow. The
      interface underwent (non-silent) changes, therefore scripts
      will have to be slightly adapted. Most notably, particle
      access by id and particle slices have a new syntax, and
      electrostatic/magnetostatic layer correction and reaction
      methods have a different setup. All errors are also now
      emitted as Python exceptions and are recoverable with minimal
      effort.  An additional focus of this release is the
      simplification of both the C++ core and the Python script
      interface to facilitate future extensions of ESPResSo.  The
      testing of ESPResSo's functionality has been extended
      considerably. We recommend that this release be used for all
      production simulations. No further bug fix releases will be
      provided for the 4.1 line, and not all fixes are present in
      ESPResSo 4.1.4.
    Added functionality
    - ------------------
    * `P3MGPU` now supports energy and pressure calculation via
      the CPU kernels (#4506).
    * `ELC` now works with `P3MGPU` (#4506).
    * The LB grid now supports slicing operations (#4195) and LB
      slices are equality comparable (#4268).
    * Lees-Edwards boundary conditions can be used for
      particle-based simulations (#4457). Lattice-Boltzmann
      support will be added in the 4.3.0 release.
    * The non-bonded energy of a single particle can be calculated
      (#4401).
    * The list of close neighbors of a single particle can be
      extracted (#4401).
    * Brownian Dynamics simulations can be carried out with the
      newly added Brownian integrator and Brownian thermostat
      (#1842).
    * Stokesian Dynamics simulations can be carried out with the
      newly added Stokesian integrator and Stokesian thermostat
      (#3790, #3987).
    * Bonded interactions can now be automatically broken when the
      bond length exceeds a critical value (#4456). This feature
      can be combined with collision detection to model reversible
      bonds (#4464).
    * A new cell system `HybridDecomposition` was introduced to
      speed up simulations with inhomogeneous particle interaction
      ranges (#4373).
    * Shapes can be merged into meta-shapes (#3493, #3538).
    * The `HollowConicalFrustum` can now be sliced open, made
      thick and rotated to model quarter pipes in any orientation
      (#4179). The main application is in the construction of
      complex microchannel geometries via `LBBoundaries`.
    * A parametric weight function was added to the DPD
      interaction (#3570).
    * H5MD output files now support a unit system (#3751).
    * H5MD output files now support custom specifications to
      control which particle and box properties to write to disk
      (#4480).
    * The `H5md` class is now checkpointable and usable in an
      interactive Python session (#3751).
    * MDAnalysis integration now provides bond information
      (#3801).
  - Give up on building on 32bit architectures (gh#espressomd/espresso#4537).
  - Fix rpath in provided libraries and shebang in pypresso.
* Sat Apr 16 2022 Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
  - added rpath.patch to fix the failing Rpath checks (see
    boo#1198352)
* Sat Apr 16 2022 Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
  - added hdf5.patch to fix builds with H5MD (see
    gh#espressomd/espresso#3543)
* Mon Jul 12 2021 Christoph Junghans <junghans@votca.org>
  - added missing_size_t.patch, to workaround missing size_t (see
    gh#espressomd/espresso#4274)
* Tue May 11 2021 Dominique Leuenberger <dimstar@opensuse.org>
  - Use openmpi4 on 'non-sle based systems' (aka Tumbleweed) (can't
    use unversioned openmpi, as hdf5-openmpi-devel would not exist).
* Thu Oct 29 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 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 08 2020 Christoph Junghans <junghans@votca.org>
  - fix unversioned Obsoletes: statement
* Fri Aug 21 2020 Christoph Junghans <junghans@votca.org>
  - force the use of shared hdf5 by setting HDF5_USE_SHLIB
* Wed Jul 08 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 2020 Christoph Junghans <junghans@votca.org>
  - Require: the right hdf5 library
* Mon May 11 2020 Christoph Junghans <junghans@votca.org>
  - enable hdf5 support
  - python3-numpy & python3-h5md are needed at runtime
* Tue Jan 21 2020 Christoph Junghans <junghans@votca.org>
  - add 3427.patch to fix tests on i586
* Wed Jan 15 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 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 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 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

Files

/usr/bin/pypresso
/usr/lib64/python3.10/site-packages/espressomd
/usr/lib64/python3.10/site-packages/espressomd/Espresso_config.so
/usr/lib64/python3.10/site-packages/espressomd/Espresso_core.so
/usr/lib64/python3.10/site-packages/espressomd/Espresso_script_interface.so
/usr/lib64/python3.10/site-packages/espressomd/Espresso_shapes.so
/usr/lib64/python3.10/site-packages/espressomd/MDA_ESP
/usr/lib64/python3.10/site-packages/espressomd/MDA_ESP/__init__.py
/usr/lib64/python3.10/site-packages/espressomd/__cinit__.py
/usr/lib64/python3.10/site-packages/espressomd/__init__.py
/usr/lib64/python3.10/site-packages/espressomd/_init.so
/usr/lib64/python3.10/site-packages/espressomd/accumulators.py
/usr/lib64/python3.10/site-packages/espressomd/actors.py
/usr/lib64/python3.10/site-packages/espressomd/analyze.so
/usr/lib64/python3.10/site-packages/espressomd/bond_breakage.py
/usr/lib64/python3.10/site-packages/espressomd/cell_system.py
/usr/lib64/python3.10/site-packages/espressomd/checkpointing.py
/usr/lib64/python3.10/site-packages/espressomd/cluster_analysis.py
/usr/lib64/python3.10/site-packages/espressomd/code_info.so
/usr/lib64/python3.10/site-packages/espressomd/collision_detection.py
/usr/lib64/python3.10/site-packages/espressomd/comfixed.py
/usr/lib64/python3.10/site-packages/espressomd/constraints.py
/usr/lib64/python3.10/site-packages/espressomd/cuda_init.so
/usr/lib64/python3.10/site-packages/espressomd/drude_helpers.py
/usr/lib64/python3.10/site-packages/espressomd/ekboundaries.py
/usr/lib64/python3.10/site-packages/espressomd/electrokinetics.so
/usr/lib64/python3.10/site-packages/espressomd/electrostatic_extensions.py
/usr/lib64/python3.10/site-packages/espressomd/electrostatics.py
/usr/lib64/python3.10/site-packages/espressomd/galilei.so
/usr/lib64/python3.10/site-packages/espressomd/gen_code_info.py
/usr/lib64/python3.10/site-packages/espressomd/gen_pxiconfig.py
/usr/lib64/python3.10/site-packages/espressomd/highlander.py
/usr/lib64/python3.10/site-packages/espressomd/integrate.so
/usr/lib64/python3.10/site-packages/espressomd/interactions.so
/usr/lib64/python3.10/site-packages/espressomd/io
/usr/lib64/python3.10/site-packages/espressomd/io/__init__.py
/usr/lib64/python3.10/site-packages/espressomd/io/mpiio.py
/usr/lib64/python3.10/site-packages/espressomd/io/writer
/usr/lib64/python3.10/site-packages/espressomd/io/writer/__init__.py
/usr/lib64/python3.10/site-packages/espressomd/io/writer/h5md.py
/usr/lib64/python3.10/site-packages/espressomd/io/writer/vtf.py
/usr/lib64/python3.10/site-packages/espressomd/lb.so
/usr/lib64/python3.10/site-packages/espressomd/lbboundaries.py
/usr/lib64/python3.10/site-packages/espressomd/lees_edwards.py
/usr/lib64/python3.10/site-packages/espressomd/magnetostatics.py
/usr/lib64/python3.10/site-packages/espressomd/math.py
/usr/lib64/python3.10/site-packages/espressomd/observables.py
/usr/lib64/python3.10/site-packages/espressomd/pair_criteria.py
/usr/lib64/python3.10/site-packages/espressomd/particle_data.so
/usr/lib64/python3.10/site-packages/espressomd/polymer.so
/usr/lib64/python3.10/site-packages/espressomd/profiler.so
/usr/lib64/python3.10/site-packages/espressomd/reaction_methods.py
/usr/lib64/python3.10/site-packages/espressomd/rotation.py
/usr/lib64/python3.10/site-packages/espressomd/script_interface.so
/usr/lib64/python3.10/site-packages/espressomd/shapes.py
/usr/lib64/python3.10/site-packages/espressomd/system.so
/usr/lib64/python3.10/site-packages/espressomd/thermostat.so
/usr/lib64/python3.10/site-packages/espressomd/utils.so
/usr/lib64/python3.10/site-packages/espressomd/version.so
/usr/lib64/python3.10/site-packages/espressomd/virtual_sites.py
/usr/lib64/python3.10/site-packages/espressomd/visualization.py
/usr/share/doc/packages/python3-espressomd
/usr/share/doc/packages/python3-espressomd/AUTHORS
/usr/share/doc/packages/python3-espressomd/ChangeLog
/usr/share/doc/packages/python3-espressomd/NEWS
/usr/share/doc/packages/python3-espressomd/Readme.md
/usr/share/licenses/python3-espressomd
/usr/share/licenses/python3-espressomd/COPYING


Generated by rpm2html 1.8.1

Fabrice Bellet, Tue Mar 12 00:04:49 2024