- 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)
OBS-URL: https://build.opensuse.org/request/show/748973
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=9
- 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)
OBS-URL: https://build.opensuse.org/request/show/699758
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=7
- 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
- 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
- add 1830.patch to fix install
- update version 3.3.1+git20180203.f74064d
* many many small fixes
* support for newer cython
- adapt to new openlmi package - source mpivars.h during build
- use individual libboost-*-devel packages instead of boost-devel
- RPM group fixup
- 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
- 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
- Update to version 3.3.1
* A lot of changes; please read the NEWS file
- 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
- build openmpi and non-mpi version
- initial commit
OBS-URL: https://build.opensuse.org/request/show/642286
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=1
- 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
- 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
- add 1830.patch to fix install
- update version 3.3.1+git20180203.f74064d
* many many small fixes
* support for newer cython
- adapt to new openlmi package - source mpivars.h during build
- use individual libboost-*-devel packages instead of boost-devel
- RPM group fixup
- 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
- 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
- Update to version 3.3.1
* A lot of changes; please read the NEWS file
- 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
- build openmpi and non-mpi version
- initial commit
OBS-URL: https://build.opensuse.org/request/show/642129
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=1
