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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
#
Accepting request 1143707 from home:jngrad:branches:devel:languages:python:numeric Fix undefined behavior OBS-URL: https://build.opensuse.org/request/show/1143707 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=51
2024-02-02 18:29:05 +01:00
# spec file for package python3-espressomd
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
#
Accepting request 1143707 from home:jngrad:branches:devel:languages:python:numeric Fix undefined behavior OBS-URL: https://build.opensuse.org/request/show/1143707 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=51
2024-02-02 18:29:05 +01:00
# Copyright (c) 2024 SUSE LLC
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
# Copyright (c) 2014 Christoph Junghans
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
Accepting request 764818 from home:mcepl:branches:devel:languages:python:numeric - 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 OBS-URL: https://build.opensuse.org/request/show/764818 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=11
2020-01-16 00:27:06 +01:00
Accepting request 748973 from home:cjunghans:branches:devel:languages:python:numeric - 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
2019-11-18 08:48:49 +01:00
# Build with OpenMPI
Accepting request 892207 from home:dimstar:Factory Fix build in Tumbleweed OBS-URL: https://build.opensuse.org/request/show/892207 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=27
2021-05-11 14:44:12 +02:00
%define mpiver openmpi4
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
%define pkgname espresso
%define modname %{pkgname}md
Name: python3-%{modname}
Accepting request 1175904 from home:jngrad:branches:devel:languages:python:numeric ESPResSo 4.2.2 OBS-URL: https://build.opensuse.org/request/show/1175904 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=53
2024-05-22 21:37:29 +02:00
Version: 4.2.2
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
Release: 0
Summary: Parallel simulation software for soft matter research
License: GPL-3.0-or-later
URL: http://espressomd.org
Source: https://github.com/%{modname}/%{pkgname}/releases/download/%{version}/%{pkgname}-%{version}.tar.gz
- Give up on building on 32bit architectures (gh#espressomd/espresso#4537). OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=35
2022-07-20 23:36:44 +02:00
# According to gh#espressomd/espresso#4537 32bit architectures are not supported any more
Accepting request 1175904 from home:jngrad:branches:devel:languages:python:numeric ESPResSo 4.2.2 OBS-URL: https://build.opensuse.org/request/show/1175904 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=53
2024-05-22 21:37:29 +02:00
ExcludeArch: %{ix86} armv7l
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
BuildRequires: cmake
BuildRequires: fftw3-devel
BuildRequires: gcc-c++
# Currently libboost_mpi-devel and hdf5 use different mpi versions
# BuildRequires: hdf5-devel
Accepting request 748973 from home:cjunghans:branches:devel:languages:python:numeric - 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
2019-11-18 08:48:49 +01:00
BuildRequires: %{mpiver}-devel
- Fix rpath in provided libraries and shebang in pypresso. OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=36
2022-07-21 07:55:40 +02:00
BuildRequires: chrpath
Accepting request 764818 from home:mcepl:branches:devel:languages:python:numeric - 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 OBS-URL: https://build.opensuse.org/request/show/764818 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=11
2020-01-16 00:27:06 +01:00
BuildRequires: gsl-devel
Accepting request 892207 from home:dimstar:Factory Fix build in Tumbleweed OBS-URL: https://build.opensuse.org/request/show/892207 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=27
2021-05-11 14:44:12 +02:00
BuildRequires: hdf5-%{mpiver}-devel
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
BuildRequires: libboost_filesystem-devel
BuildRequires: libboost_mpi-devel
BuildRequires: libboost_system-devel
BuildRequires: libboost_test-devel
Accepting request 1114814 from home:mimi_vx:branches:devel:languages:python:numeric - cleanup spec - skip mpiio test OBS-URL: https://build.opensuse.org/request/show/1114814 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=49
2023-10-02 14:12:56 +02:00
BuildRequires: python3-Cython < 3
BuildRequires: python3-devel
Accepting request 802785 from home:cjunghans:branches:devel:languages:python:numeric - enable hdf5 support - python3-numpy & python3-h5md are needed at runtime - add 3427.patch to fix tests on i586 - 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) - 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) - 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) - Version bump to 4.0.1 * Many small bugfixes - Drop 2255.patch, 2259.patch and 2265.patch - merged upstream - 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/802785 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=17
2020-05-12 00:21:01 +02:00
BuildRequires: python3-h5py
Accepting request 1114814 from home:mimi_vx:branches:devel:languages:python:numeric - cleanup spec - skip mpiio test OBS-URL: https://build.opensuse.org/request/show/1114814 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=49
2023-10-02 14:12:56 +02:00
BuildRequires: python3-numpy-devel
BuildRequires: python3-scipy
BuildRequires: python3-setuptools
Accepting request 892207 from home:dimstar:Factory Fix build in Tumbleweed OBS-URL: https://build.opensuse.org/request/show/892207 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=27
2021-05-11 14:44:12 +02:00
BuildRequires: zlib-devel
- Fix rpath in provided libraries and shebang in pypresso. OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=36
2022-07-21 07:55:40 +02:00
Provides: libEspresso4 = %{version}-%{release}
Accepting request 843025 from home:cjunghans:branches:devel:languages:python:numeric - Update to 4.1.4, see https://github.com/espressomd/espresso/blob/4.1.4/NEWS for details - fix unversioned Obsoletes: statement OBS-URL: https://build.opensuse.org/request/show/843025 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=24
2020-10-20 21:21:22 +02:00
Obsoletes: libEspresso4 < 4.1
Accepting request 802785 from home:cjunghans:branches:devel:languages:python:numeric - enable hdf5 support - python3-numpy & python3-h5md are needed at runtime - add 3427.patch to fix tests on i586 - 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) - 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) - 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) - Version bump to 4.0.1 * Many small bugfixes - Drop 2255.patch, 2259.patch and 2265.patch - merged upstream - 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/802785 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=17
2020-05-12 00:21:01 +02:00
Requires: python3-h5py
Accepting request 892207 from home:dimstar:Factory Fix build in Tumbleweed OBS-URL: https://build.opensuse.org/request/show/892207 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=27
2021-05-11 14:44:12 +02:00
Requires: python3-numpy
Accepting request 808074 from home:cjunghans:branches:devel:languages:python:numeric - Require: the right hdf5 library OBS-URL: https://build.opensuse.org/request/show/808074 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=19
2020-05-22 05:55:15 +02:00
# make sure rpm pulls in the right dependency
Requires: libhdf5-%{mpiver}
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
%description
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.
%prep
- 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 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=32
2022-07-20 20:34:52 +02:00
%autosetup -p1 -n %{pkgname}
- Fix rpath in provided libraries and shebang in pypresso. OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=36
2022-07-21 07:55:40 +02:00
# Fix shebang line for pypresso
sed -i -E '1s@^#!/usr/bin/env[[:blank:]]+sh@#!/bin/sh@' src/python/pypresso.cmakein
Accepting request 1114814 from home:mimi_vx:branches:devel:languages:python:numeric - cleanup spec - skip mpiio test OBS-URL: https://build.opensuse.org/request/show/1114814 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=49
2023-10-02 14:12:56 +02:00
# skip mpiio test - it fails if inwoked with cmake, direct run with python3 -m unittest pass
sed -i '/mpiio\.py/d' testsuite/python/CMakeLists.txt
- Fix rpath in provided libraries and shebang in pypresso. OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=36
2022-07-21 07:55:40 +02:00
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
%build
Accepting request 748973 from home:cjunghans:branches:devel:languages:python:numeric - 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
2019-11-18 08:48:49 +01:00
source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh
Accepting request 764818 from home:mcepl:branches:devel:languages:python:numeric - 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 OBS-URL: https://build.opensuse.org/request/show/764818 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=11
2020-01-16 00:27:06 +01:00
# gh#espressomd/espresso#3396
%define _lto_cflags %{nil}
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
Accepting request 828547 from home:cjunghans:branches:devel:languages:python:numeric - force the use of shared hdf5 by setting HDF5_USE_SHLIB OBS-URL: https://build.opensuse.org/request/show/828547 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=22
2020-08-21 18:37:21 +02:00
#force usage of shared hdf5
export HDF5_USE_SHLIB=yes
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
# overwrite .so linker flags on SUSE distros: drop --no-undefined
# we don't install {i,}pypresso scripts as they aren't needed when installing in /usr
%cmake \
Accepting request 808074 from home:cjunghans:branches:devel:languages:python:numeric - Require: the right hdf5 library OBS-URL: https://build.opensuse.org/request/show/808074 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=19
2020-05-22 05:55:15 +02:00
-DCMAKE_SHARED_LINKER_FLAGS='-Wl,--as-needed -Wl,-z,now' \
Accepting request 1080111 from home:jngrad:branches:devel:languages:python:numeric ESPResSo 4.2.1 OBS-URL: https://build.opensuse.org/request/show/1080111 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=44
2023-04-18 22:51:28 +02:00
-DCMAKE_SKIP_RPATH=ON \
- 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 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=32
2022-07-20 20:34:52 +02:00
-DLIBDIR=%{_libdir} \
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
-DPYTHON_EXECUTABLE=%{_bindir}/python3 \
- 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 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=32
2022-07-20 20:34:52 +02:00
-DPYTHON_INSTDIR=%{python3_sitearch} \
-DINSTALL_PYPRESSO=ON
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
%make_jobs
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
%install
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
%cmake_install
- Fix rpath in provided libraries and shebang in pypresso. OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=36
2022-07-21 07:55:40 +02:00
find %{buildroot}%{python3_sitearch} -name \*.so \
-exec chrpath -r %{python3_sitearch} '{}' \;
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
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
%check
Accepting request 748973 from home:cjunghans:branches:devel:languages:python:numeric - 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
2019-11-18 08:48:49 +01:00
LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}}
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
%files
%license COPYING
- 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 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=32
2022-07-20 20:34:52 +02:00
%doc Readme.md AUTHORS NEWS ChangeLog
%{_bindir}/pypresso
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
%{python3_sitearch}/espressomd
Accepting request 764818 from home:mcepl:branches:devel:languages:python:numeric - 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 OBS-URL: https://build.opensuse.org/request/show/764818 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=11
2020-01-16 00:27:06 +01:00
%changelog
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