forked from pool/python3-espressomd
8a45f5416d
- add 3427.patch to fix tests on i586 OBS-URL: https://build.opensuse.org/request/show/766146 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=14
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-------------------------------------------------------------------
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Tue Jan 21 13:26:55 UTC 2020 - Christoph Junghans <junghans@votca.org>
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- add 3427.patch to fix tests on i586
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-------------------------------------------------------------------
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Wed Jan 15 23:35:14 CET 2020 - Matej Cepl <mcepl@suse.com>
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- Update to 4.1.2:
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- The interface has not been changed between ESPResSo 4.1.1 and
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4.1.2.
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- General corrections and improvements:
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- Remove correlation between the rotational noise and
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translational noise in the Langevin thermostat (#3355)
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- Fix a bug that may cause the wrong temperature to be set by
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the Langevin and DPD thermostats in the first time step
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after the system was altered from the Python level, e.g.,
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by changing particles or interactions (#3341)
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- Fix a bug that caused the DPD thermostat to generate an
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incorrect velocity distribution when used together with the
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Langevin thermostat (#3352)
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- Fix a bug in MMM2D and ELC with potential boundary
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conditions, where one of the correction factors was
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over-counted resulting in wrong energies (#3310)
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- Fix a bug that caused the wrong bonds to be deleted when
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removing particles from the system (#3356)
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- Fix an ambiguity in `ParticleSlice`: the values in the
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square brackets refer to particle ids, not array indices
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(#3367). This means the ill-defined syntax
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`system.part[0:-1]` is no longer valid. See the User Guide
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section on Setting up particles for more information.
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- Remove the mass prefactor in the `ComForce` observable and
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use the correct Particle ids in the
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`ParticleAngularVelocities` and `ParticleBodyVelocities`
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observables (#3380)
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- Fix a rounding error that caused debug builds of ESPResSo
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running with multiple MPI threads to crash when a particle
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was placed exactly on the boundary between two cells
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(#3377)
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- Fix `espressomd.has_features()` for the corner case where
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the list of all compiled-in features is passed as argument,
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returning ``False`` instead of ``True`` (#3318)
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- Refactor the random number generator code (#3349)
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- Documentation and tutorials corrections and improvements:
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- Improve documentation of Monte Carlo methods (#3254, #3330)
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- Build system and platform-related corrections and
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improvements:
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- List all Python dependencies in `requirements.txt` with the
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supported version numbers (#3300). Please note that most of
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them are optional.
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- Add `MPIEXEC_PREFLAGS` and `MPIEXEC_POSTFLAGS` to the
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command lines of parallel tests (#3221)
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- Add the `-oversubscribe` flag to the command lines of
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parallel tests running with OpenMPI v2.X to avoid exiting
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early from a Python test configured without `MAX_NUM_PROC`
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on a machine with a hyperthreaded CPU where OpenMPI is
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configured such that the number of threads cannot exceed
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the number of cores (#3335)
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- Refactor the CI, maintainer, Doxygen and pypresso shell
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scripts to make them more portable and support filepaths
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containing whitespaces (#3326, #3373)
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- Fix a nvcc compiler warning on the empty config (#3329)
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- Improved testing:
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- Add a test for ELC and MMM2D using analytic expressions of
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the force and energy (#3331)
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- Sped-up seven Python tests (#3319)
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- Fix a test that broke on s390x architectures with Fedora 31
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(#3312)
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- Fix tests that broke on i586 architectures with OpenSUSE
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Tumbleweed (#3327, #3358)
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-------------------------------------------------------------------
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Fri Nov 15 16:24:45 UTC 2019 - Christoph Junghans <junghans@votca.org>
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- Version bump to 4.1.1
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* Restore checkpointing mechanism for the steepest descent and NPT
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integrators, LB and NPT thermostats (#3245)
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* Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and
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lower are no longer supported (#3236)
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* Fix `Integrator.set_isotropic_npt()`: remove the silent conversion of
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the incorrect input parameter `direction=[0,0,0]` to `[1,1,1]` in the
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core; the function now throws an exception for fixed-volume boxes;
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this change is unlikely to break pypresso scripts since not providing
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a value to `direction` or providing `[1,1,1]` were the two standard
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ways to set up a box with all directions allowed to rescale (#3253)
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* Fix `Integrator.set_vv()`: this function failed to set the velocity
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Verlet integrator if the NPT integrator was active; this is now
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resolved (#3274)
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* Fix the random segmentation fault triggered by the removal of a
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particle with a bond or a virtual site relationship to another
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particle (#3288)
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* Fix `system.part.writevtk()`: the function now writes down all
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particles when using `types="all"` (#3290)
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* Disable the deprecated and broken ENGINE shear torque calculation
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feature; the feature will be completely removed from the core in
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the upcoming 4.2 release (#3277)
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* Fix unit conversion for the LB fluid viscosity (#3287)
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-------------------------------------------------------------------
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Tue Apr 30 18:06:33 UTC 2019 - Christoph Junghans <junghans@votca.org>
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- Version bump to 4.0.2
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*Corrections for bugs that may harm simulation results:
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* A sign error in tabulated interactions was corrected such that
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the force equals the negative gradient of the potential.
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(#2519,2520)
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* The flow field of the CPU lattice-Boltzmann implementation was
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deleted when aspects of the molecular dynamics cell grid were
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changed; E.g., when interactions, the skin or the parallelization
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setup were changed. ESPResSo now terminates with an error, when this
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happens. To avoid this, please setup the CPU lattice-Boltzmann after
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all other aspects of the system. The GPU LB is not affected in the
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4.0 release, but was affected in the current development branch.
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(#2728, #2736)
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* Corrected the force acting on LB Boundaries for the case of
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agrid and density not equal to 1 (#2624).
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* Corrected the cutoff calculation for the soft sphere interaction. In
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the previous implementation, the offset parameter was ignored.
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(#2505)
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* The "three point coupling" of particles to the lattice-Boltzmann
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method has been removed. While it works in most environments, for
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some compilers the calculation gives wrong values. This is likely
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caused by undefined behavior. A corrected implementation is
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available in ESPResSo's development branch. It cannot be safely
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backported to 4.0.2, because the code has diverged too far. (#2516,
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#2517) Users who did not explicitly activate this coupling via
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couple="3pt" are not affected.
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* The velocity of existing particles was changed when setting or
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changing the simulation time step (#2480)
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* Further changes:
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* Fixed the electrokinetic Python interface (#2486)
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* Correction to the installation instructions for mac (#2510)
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* Corrected file permissions (#2470)
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* Minor corrections and extensions to the test suite (#2477, #2552)
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* Fixed a dead-lock in the dipolar Barnes Hutt method on the GPU for
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recent NVIDIA cards such as RTX 2080 (#2719).
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* Restored Mayavi visualizer's API-compatibility with OpenGL
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visualizer (#2751)
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-------------------------------------------------------------------
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Fri Jan 25 16:28:37 UTC 2019 - Christoph Junghans <junghans@votca.org>
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- Version bump to 4.0.1
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* Many small bugfixes
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- Drop 2255.patch, 2259.patch and 2265.patch - merged upstream
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-------------------------------------------------------------------
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Fri Sep 28 23:13:13 UTC 2018 - Christoph Junghans <junghans@votca.org>
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- added change from request #639007
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- rename package to python3-espressomd
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- install COPYING for all packages
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- change license to GPL-3.0-or-later
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- added sonum define
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-------------------------------------------------------------------
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Fri Sep 7 15:36:54 UTC 2018 - junghans@votca.org
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- Version bump to 4.0.0
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- Rename pacakge to python-espressomd
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- Dropped 1830.patch - merged upstream
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- Dropped doc package - under rework in 4.0.0
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- New features:
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- Reaction ensemble methods for the modelling of chemical reactions, including constant pH and Wang-Landau schemes.
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- Polarisable particles via the Drude-oscillator scheme.
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- Steepest-descent energy minimization scheme.
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- Methods for active particles (swimmer_reaction, dipolar swimmers).
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- GPU-accelerated P3M method for electrostatic interactions.
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- GPU-accelerated direct summation and Barnes-Hutt schemes for dipolar interactions under open boundary conditions.
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- Support for the electrostatic and magnetostatics method provided by the ScaFaCoS library.
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- Immersed boundary method for soft immersed objects in an LB fluid.
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- Virtual sites acting as inertialess tracers in an LB fluid usable as part of the immersed boundary method or independently.
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- New bonded quartic and Coulomb interactions.
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- Possibility to tune the skin parameter.
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- Support for saving to the h5md file format for molecular dynamics data.
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- Connection to the MD Analysis Python package.
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- A rotate_system command was added, which rotates the particle positions around the system’s center of mass.
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- Added 2255.patch to fix numpy issue on i586
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- Added 2259.patch to fix numpy issue on big-endian platforms
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- Added 2265.patch to fix test on i586
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-------------------------------------------------------------------
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Mon Feb 12 19:25:01 UTC 2018 - junghans@votca.org
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- add 1830.patch to fix install
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- update version 3.3.1+git20180203.f74064d
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* many many small fixes
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* support for newer cython
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-------------------------------------------------------------------
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Wed Oct 25 12:43:08 UTC 2017 - junghans@votca.org
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- adapt to new openlmi package - source mpivars.h during build
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-------------------------------------------------------------------
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Wed Feb 1 10:36:28 UTC 2017 - adam.majer@suse.de
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- use individual libboost-*-devel packages instead of boost-devel
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-------------------------------------------------------------------
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Thu Sep 29 13:46:20 UTC 2016 - jengelh@inai.de
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- RPM group fixup
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-------------------------------------------------------------------
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Wed Aug 3 17:54:16 UTC 2016 - junghans@votca.org
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- switched to cmake build-system
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- build python module
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- dropped header as they are for internal use only
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- dropped pkg-config files as nothing depends on libs yet
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- update version 3.3.1+git20160803.6ed0518.tar.gz
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* overhaul of buildsystem
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* many many small fixes
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-------------------------------------------------------------------
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Sun Jun 26 07:35:00 UTC 2016 - i@marguerite.su
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- fix boo#985147
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* there's a commit that removed redefinition of malloc and realloc
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which fixed build for gcc 6. but it's too hard to cherry pick, so
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update to the latest git version is a good idea
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- there's no --without-mpi option left in configure.ac, so "-openmpi"
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sub-package is meaningless now (everything has openmpi support)
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and since there's no two main packages any more, "-common" sub-package
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is also meaningless now (and it doesn't contains data), merged.
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- add sub-package: "-devel", "libEspresso0", "libEspressoTcl0"
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- add generate_headers.rb to gather those .hpp that're really used
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into "-devel" sub-package
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- create pkgconfig files
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- add some texlive BuildRequires to build pdf documentation.
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- update version 3.3.1+git20160622.6aa229c:
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* added edge statistics for meshes used by object-in-fluid
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* added pos_folded property
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* Adapted simple LB tests to current interface.
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* system.part.writevtk()
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* redesigned exclusions and added slice input
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* Scafacos: Add long range energy to correct place in energy data structure
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* Correction to scafacos energy calculation: Check cutoff in near field contrib
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* Scafacos: Sort out conditional compilation and cython includes
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* Scafacos: methods shared between electrostatics and dipolar calculations
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-------------------------------------------------------------------
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Sun Nov 8 21:57:37 UTC 2015 - p.drouand@gmail.com
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- Update to version 3.3.1
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* A lot of changes; please read the NEWS file
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-------------------------------------------------------------------
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Tue Aug 12 03:44:16 UTC 2014 - junghans@votca.org
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- version bumped to 3.3.0
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- Highlights of this release include:
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- Calculation of the electrokinetic equations via the ELECTROKINETICS feature,
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- the Shan/Chen method for multi component lattice Boltzmann fluids,
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- the P3M and MMM1D methods can now be computed on a GPU,
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- ESPResSo now has a rudimentary Python interface.
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For a complete list of the changes in the release, please refer to:
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http://download.savannah.gnu.org/releases/espressomd/NEWS
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-------------------------------------------------------------------
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Fri Feb 7 17:41:18 UTC 2014 - junghans@votca.org
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- build openmpi and non-mpi version
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-------------------------------------------------------------------
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Tue Feb 4 18:59:10 UTC 2014 - junghans@votca.org
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- initial commit
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