From f05e7b8e0b434f9adf38d5daba17f5c0e19d9168aadcf135ed9cf0e1051fb27a Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 15 Jan 2020 23:27:06 +0000 Subject: [PATCH] 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 This means the ill-defined syntax `system.part[0:-1]` is no longer valid.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 --- espresso-4.1.1.tar.gz | 3 -- espresso-4.1.2.tar.gz | 3 ++ python3-espressomd.changes | 66 ++++++++++++++++++++++++++++++++++++++ python3-espressomd.spec | 11 ++++--- 4 files changed, 76 insertions(+), 7 deletions(-) delete mode 100644 espresso-4.1.1.tar.gz create mode 100644 espresso-4.1.2.tar.gz diff --git a/espresso-4.1.1.tar.gz b/espresso-4.1.1.tar.gz deleted file mode 100644 index 28efde2..0000000 --- a/espresso-4.1.1.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:61f19f17469522d4aa480ff5254217668ba713589c6b74576e6305920d688f90 -size 22915050 diff --git a/espresso-4.1.2.tar.gz b/espresso-4.1.2.tar.gz new file mode 100644 index 0000000..7428eb8 --- /dev/null +++ b/espresso-4.1.2.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:00bc8e4cab8fc8f56d18978970b55f09168521ed5898a92769986f2157a81a2c +size 22921088 diff --git a/python3-espressomd.changes b/python3-espressomd.changes index 741124f..e84e70a 100644 --- a/python3-espressomd.changes +++ b/python3-espressomd.changes @@ -1,3 +1,69 @@ +------------------------------------------------------------------- +Wed Jan 15 23:35:14 CET 2020 - Matej Cepl + +- Update to 4.1.2: + - The interface has not been changed between ESPResSo 4.1.1 and + 4.1.2. + - General corrections and improvements: + - Remove correlation between the rotational noise and + translational noise in the Langevin thermostat (#3355) + - Fix a bug that may cause the wrong temperature to be set by + the Langevin and DPD thermostats in the first time step + after the system was altered from the Python level, e.g., + by changing particles or interactions (#3341) + - Fix a bug that caused the DPD thermostat to generate an + incorrect velocity distribution when used together with the + Langevin thermostat (#3352) + - Fix a bug in MMM2D and ELC with potential boundary + conditions, where one of the correction factors was + over-counted resulting in wrong energies (#3310) + - Fix a bug that caused the wrong bonds to be deleted when + removing particles from the system (#3356) + - Fix an ambiguity in `ParticleSlice`: the values in the + square brackets refer to particle ids, not array indices + (#3367). This means the ill-defined syntax + `system.part[0:-1]` is no longer valid. See the User Guide + section on Setting up particles for more information. + - Remove the mass prefactor in the `ComForce` observable and + use the correct Particle ids in the + `ParticleAngularVelocities` and `ParticleBodyVelocities` + observables (#3380) + - Fix a rounding error that caused debug builds of ESPResSo + running with multiple MPI threads to crash when a particle + was placed exactly on the boundary between two cells + (#3377) + - Fix `espressomd.has_features()` for the corner case where + the list of all compiled-in features is passed as argument, + returning ``False`` instead of ``True`` (#3318) + - Refactor the random number generator code (#3349) + - Documentation and tutorials corrections and improvements: + - Improve documentation of Monte Carlo methods (#3254, #3330) + - Build system and platform-related corrections and + improvements: + - List all Python dependencies in `requirements.txt` with the + supported version numbers (#3300). Please note that most of + them are optional. + - Add `MPIEXEC_PREFLAGS` and `MPIEXEC_POSTFLAGS` to the + command lines of parallel tests (#3221) + - Add the `-oversubscribe` flag to the command lines of + parallel tests running with OpenMPI v2.X to avoid exiting + early from a Python test configured without `MAX_NUM_PROC` + on a machine with a hyperthreaded CPU where OpenMPI is + configured such that the number of threads cannot exceed + the number of cores (#3335) + - Refactor the CI, maintainer, Doxygen and pypresso shell + scripts to make them more portable and support filepaths + containing whitespaces (#3326, #3373) + - Fix a nvcc compiler warning on the empty config (#3329) + - Improved testing: + - Add a test for ELC and MMM2D using analytic expressions of + the force and energy (#3331) + - Sped-up seven Python tests (#3319) + - Fix a test that broke on s390x architectures with Fedora 31 + (#3312) + - Fix tests that broke on i586 architectures with OpenSUSE + Tumbleweed (#3327, #3358) + ------------------------------------------------------------------- Fri Nov 15 16:24:45 UTC 2019 - Christoph Junghans diff --git a/python3-espressomd.spec b/python3-espressomd.spec index 4cfc51f..e6f5e3d 100644 --- a/python3-espressomd.spec +++ b/python3-espressomd.spec @@ -1,7 +1,7 @@ # # spec file for package python3-espressomd # -# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2020 SUSE LLC # Copyright (c) 2014 Christoph Junghans # # All modifications and additions to the file contributed by third parties @@ -16,6 +16,7 @@ # Please submit bugfixes or comments via https://bugs.opensuse.org/ # + # Build with OpenMPI %if 0%{?sle_version} == 0 %define mpiver openmpi2 @@ -34,7 +35,7 @@ %define pkgname espresso %define modname %{pkgname}md Name: python3-%{modname} -Version: 4.1.1 +Version: 4.1.2 Release: 0 Summary: Parallel simulation software for soft matter research License: GPL-3.0-or-later @@ -46,8 +47,8 @@ BuildRequires: fftw3-devel BuildRequires: gcc-c++ # Currently libboost_mpi-devel and hdf5 use different mpi versions # BuildRequires: hdf5-devel -BuildRequires: gsl-devel BuildRequires: %{mpiver}-devel +BuildRequires: gsl-devel BuildRequires: python3-Cython BuildRequires: python3-devel BuildRequires: python3-numpy-devel @@ -74,6 +75,8 @@ systems, for example DNA and lipid membranes. %build source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh +# gh#espressomd/espresso#3396 +%define _lto_cflags %{nil} # 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 @@ -105,4 +108,4 @@ LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc %doc README AUTHORS NEWS ChangeLog %{python3_sitearch}/espressomd -%changelog \ No newline at end of file +%changelog