Accepting request 699758 from home:cjunghans:branches:devel:languages:python:numeric
- 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
2019-05-01 17:33:30 +02:00
|
|
|
|
-------------------------------------------------------------------
|
|
|
|
|
|
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)
|
|
|
|
|
|
|
2019-01-25 22:12:19 +01:00
|
|
|
|
-------------------------------------------------------------------
|
|
|
|
|
|
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
|
|
|
|
|
|
|
Accepting request 642129 from home:cjunghans:branches:devel:languages:python
- 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
2018-10-16 10:05:48 +02:00
|
|
|
|
-------------------------------------------------------------------
|
|
|
|
|
|
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
|
|
|
|
|
|
|
