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- Update to 4.2.0:

Browse Source 
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
This commit is contained in:
Matej Cepl 2022-07-20 18:34:52 +00:00 committed by Git OBS Bridge
parent 78e7ea8a32
commit efe8c56fdf
8 changed files with 116 additions and 54 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
boost-1.74.patch
View File

@ -10,14 +10,16 @@ including <boost/serialization/optional.hpp>. More details in tickets:
https://github.com/boostorg/serialization/issues/210
https://github.com/boostorg/serialization/issues/217
diff --git a/src/core/grid_based_algorithms/lb_particle_coupling.hpp b/src/core/grid_based_algorithms/lb_particle_coupling.hpp
index de12cb4..13111ab 100644
---
src/core/grid_based_algorithms/lb_particle_coupling.hpp | 9 +++++++++
1 file changed, 9 insertions(+)
--- a/src/core/grid_based_algorithms/lb_particle_coupling.hpp
+++ b/src/core/grid_based_algorithms/lb_particle_coupling.hpp
@@ -21,6 +21,15 @@
#include "ParticleRange.hpp"
@@ -25,6 +25,15 @@
#include <boost/serialization/access.hpp>
+/* This <boost/serialization/version.hpp> include guards against an issue
+ * in boost::serialization from boost 1.74.0 that leads to compiler error
+ * "explicit specialization of undeclared template struct 'version'" when
@ -27,6 +29,6 @@ index de12cb4..13111ab 100644
+ */
+#include <boost/serialization/version.hpp>
+
#include <boost/serialization/optional.hpp>
#include "ParticleRange.hpp"
#include <cstdint>
#include <unordered_set>

3
espresso-4.1.4.tar.gz
View File

@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:c1b68de63755475c5eb3ae8117d8c6d96c8ac36cc0f46dd44417a8e7ebe9242c
size 16950522

3
espresso-4.2.0.tar.gz Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:080bbf6bec5456192ce4e1bc0ddebb9e8735db723d3062ec87154f1ac411aaab
size 14000445

17
hdf5.patch
View File

@ -1,14 +1,17 @@
diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
index c956b9de1..b68208eaa 100644
---
src/core/CMakeLists.txt | 4 ++++
1 file changed, 4 insertions(+)
--- a/src/core/CMakeLists.txt
+++ b/src/core/CMakeLists.txt
@@ -189,6 +189,9 @@ endif(SCAFACOS)
# Subdirectories
add_subdirectory(io)
@@ -127,6 +127,10 @@ add_subdirectory(reaction_methods)
add_subdirectory(scafacos)
add_subdirectory(virtual_sites)
+if(H5MD)
+ target_link_libraries(EspressoCore PUBLIC ${HDF5_LIBRARIES})
+endif(H5MD)
if(WITH_UNIT_TESTS)
+
if(WITH_TESTS)
add_subdirectory(unit_tests)
endif(WITH_TESTS)

20
missing_size_t.patch
View File

@ -1,5 +1,7 @@
diff --git a/src/config/config.hpp b/src/config/config.hpp
index 78ec14b78..139c1f97a 100644
---
src/config/config.hpp | 2 ++
1 file changed, 2 insertions(+)
--- a/src/config/config.hpp
+++ b/src/config/config.hpp
@@ -37,6 +37,8 @@
@ -10,16 +12,4 @@ index 78ec14b78..139c1f97a 100644
+
#include "config-features.hpp"
/** P3M: Default for number of interpolation points of the charge
diff --git a/src/utils/include/utils/NumeratedContainer.hpp b/src/utils/include/utils/NumeratedContainer.hpp
index 1d99098f0..36602b203 100644
--- a/src/utils/include/utils/NumeratedContainer.hpp
+++ b/src/utils/include/utils/NumeratedContainer.hpp
@@ -25,6 +25,7 @@
*/
#include <cassert>
+#include <cstddef>
#include <set>
#include <unordered_map>
/** P3M: Default for offset of first mesh point from the origin (left

68
python3-espressomd.changes
View File

@ -1,3 +1,71 @@
-------------------------------------------------------------------
Tue Jul 19 19:40:59 UTC 2022 - Matej Cepl <mcepl@suse.com>
- 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
support will be added in the 4.3.0 release.
* The non-bonded energy of a single particle can be calculated
(#4401).
* The list of close neighbors of a single particle can be
extracted (#4401).
* Brownian Dynamics simulations can be carried out with the
newly added Brownian integrator and Brownian thermostat
(#1842).
* Stokesian Dynamics simulations can be carried out with the
newly added Stokesian integrator and Stokesian thermostat
(#3790, #3987).
* Bonded interactions can now be automatically broken when the
bond length exceeds a critical value (#4456). This feature
can be combined with collision detection to model reversible
bonds (#4464).
* A new cell system `HybridDecomposition` was introduced to
speed up simulations with inhomogeneous particle interaction
ranges (#4373).
* Shapes can be merged into meta-shapes (#3493, #3538).
* The `HollowConicalFrustum` can now be sliced open, made
thick and rotated to model quarter pipes in any orientation
(#4179). The main application is in the construction of
complex microchannel geometries via `LBBoundaries`.
* A parametric weight function was added to the DPD
interaction (#3570).
* H5MD output files now support a unit system (#3751).
* H5MD output files now support custom specifications to
control which particle and box properties to write to disk
(#4480).
* The `H5md` class is now checkpointable and usable in an
interactive Python session (#3751).
* MDAnalysis integration now provides bond information
(#3801).
-------------------------------------------------------------------
Sat Apr 16 00:24:21 UTC 2022 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>

21
python3-espressomd.spec
View File

@ -35,7 +35,7 @@
%define pkgname espresso
%define modname %{pkgname}md
Name: python3-%{modname}
Version: 4.1.4
Version: 4.2.0
Release: 0
Summary: Parallel simulation software for soft matter research
License: GPL-3.0-or-later
@ -60,6 +60,8 @@ BuildRequires: gsl-devel
BuildRequires: python3-Cython
BuildRequires: python3-devel
BuildRequires: python3-numpy-devel
BuildRequires: python3-scipy
BuildRequires: python3-setuptools
%if 0%{?suse_version} > 1325
BuildRequires: hdf5-%{mpiver}-devel
BuildRequires: libboost_filesystem-devel
@ -86,11 +88,7 @@ such as polymers, liquid crystals, colloids, ferrofluids and biological
systems, for example DNA and lipid membranes.
%prep
%setup -q -n %{pkgname}
%patch0 -p1
%patch1 -p1
%patch2 -p1
%patch3 -p1
%autosetup -p1 -n %{pkgname}
%build
source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh
@ -103,17 +101,15 @@ export HDF5_USE_SHLIB=yes
# we don't install {i,}pypresso scripts as they aren't needed when installing in /usr
%cmake \
-DCMAKE_SHARED_LINKER_FLAGS='-Wl,--as-needed -Wl,-z,now' \
-DLIBDIR=%{_lib} \
-DLIBDIR=%{_libdir} \
-DPYTHON_EXECUTABLE=%{_bindir}/python3 \
-DINSTALL_PYPRESSO=OFF
-DPYTHON_INSTDIR=%{python3_sitearch} \
-DINSTALL_PYPRESSO=ON
%make_jobs
%install
%cmake_install
# no devel package
rm -f %{buildroot}%{_libdir}/lib*.so
%check
# gh#espressomd/espresso#3315
%ifarch i586
@ -123,7 +119,8 @@ LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc
%files
%license COPYING
%doc README AUTHORS NEWS ChangeLog
%doc Readme.md AUTHORS NEWS ChangeLog
%{_bindir}/pypresso
%{python3_sitearch}/espressomd
%changelog

18
rpath.patch
View File

@ -1,13 +1,15 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 238e6dac3..96cbaa9a9 100644
---
CMakeLists.txt | 2 ++
1 file changed, 2 insertions(+)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -20,6 +20,7 @@
@@ -21,6 +21,8 @@
cmake_minimum_required(VERSION 3.4)
cmake_minimum_required(VERSION 3.16)
message(STATUS "CMake version: ${CMAKE_VERSION}")
+set(CMAKE_SKIP_RPATH ON)
# C++ standard
enable_language(CXX)
+
if(POLICY CMP0076)
# make target_sources() convert relative paths to absolute
cmake_policy(SET CMP0076 NEW)