diff --git a/.gitignore b/.gitignore
index be8aa67..0302787 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@
 /espresso-4.0.0.tar.gz
 /espresso-4.0.1.tar.gz
 /espresso-4.0.2.tar.gz
+/espresso-4.1.0.tar.gz
diff --git a/2946.patch b/2946.patch
deleted file mode 100644
index e574302..0000000
--- a/2946.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From 1acce67ef18bc7cff34f8f0d8455dd1e7e38812c Mon Sep 17 00:00:00 2001
-From: Christoph Junghans <junghans@lanl.gov>
-Date: Wed, 26 Jun 2019 11:57:51 -0600
-Subject: [PATCH 1/2] cmake: add soversion to libH5mdCore
-
----
- src/core/io/writer/CMakeLists.txt | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/core/io/writer/CMakeLists.txt b/src/core/io/writer/CMakeLists.txt
-index d0256da721..b0ce2c1d4a 100644
---- a/src/core/io/writer/CMakeLists.txt
-+++ b/src/core/io/writer/CMakeLists.txt
-@@ -7,5 +7,6 @@ target_include_directories(H5mdCore SYSTEM PUBLIC
- 
- add_dependencies(H5mdCore EspressoConfig)
- target_include_directories(H5mdCore PRIVATE ${CMAKE_SOURCE_DIR}/src/core ${CMAKE_BINARY_DIR}/src/core)
-+set_target_properties(H5mdCore PROPERTIES SOVERSION ${SOVERSION})
- install(TARGETS H5mdCore LIBRARY DESTINATION ${LIBDIR})
- endif()
-
diff --git a/3228.diff b/3228.diff
new file mode 100644
index 0000000..812096a
--- /dev/null
+++ b/3228.diff
@@ -0,0 +1,139 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 55ceaaf2bc..f6409ffcc1 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -29,14 +29,6 @@ endif()
+ enable_language(CXX)
+ 
+ set(PROJECT_VERSION "4.1.0")
+-string(REGEX
+-       REPLACE "^([1-9]+)\\.[0-9]+.*$"
+-               "\\1"
+-               SOVERSION
+-               "${PROJECT_VERSION}")
+-if(NOT ${SOVERSION} MATCHES "^[1-9]+$")
+-  message(FATAL_ERROR "Could not determine SOVERSION from ${PROJECT_VERSION}")
+-endif(NOT ${SOVERSION} MATCHES "^[1-9]+$")
+ 
+ #
+ # CMake internal vars
+diff --git a/doc/sphinx/conf.py.in b/doc/sphinx/conf.py.in
+index cb0b3c6757..abe304110b 100644
+--- a/doc/sphinx/conf.py.in
++++ b/doc/sphinx/conf.py.in
+@@ -69,7 +69,7 @@ author = 'C. Holm, F. Weik, R. Weeber'
+ # The short X.Y version.
+ version = '@PROJECT_VERSION@'
+ # The full version, including alpha/beta/rc tags.
+-release = '@SOVERSION@'
++release = '@PROJECT_VERSION@'
+ 
+ # The language for content autogenerated by Sphinx. Refer to documentation
+ # for a list of supported languages.
+diff --git a/src/config/CMakeLists.txt b/src/config/CMakeLists.txt
+index 618e4e59c6..dd34cb4b97 100644
+--- a/src/config/CMakeLists.txt
++++ b/src/config/CMakeLists.txt
+@@ -36,7 +36,6 @@ execute_process(COMMAND ${PYTHON_EXECUTABLE}
+ add_library(EspressoConfig SHARED config-features.cpp)
+ add_dependencies(EspressoConfig myconfig check_myconfig generate_config_features)
+ install(TARGETS EspressoConfig LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+-set_target_properties(EspressoConfig PROPERTIES SOVERSION ${SOVERSION})
+ target_include_directories(EspressoConfig PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
+ 
+ # Parse repository info from git if available
+diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
+index de03ad86f8..c956b9de16 100644
+--- a/src/core/CMakeLists.txt
++++ b/src/core/CMakeLists.txt
+@@ -158,7 +158,6 @@ else(CUDA)
+ endif(CUDA)
+ 
+ install(TARGETS EspressoCore LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+-set_target_properties(EspressoCore PROPERTIES SOVERSION ${SOVERSION})
+ target_include_directories(EspressoCore PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+ if(WITH_COVERAGE)
+   target_compile_options(EspressoCore PUBLIC "$<$<CONFIG:Release>:-g>")
+diff --git a/src/core/cluster_analysis/CMakeLists.txt b/src/core/cluster_analysis/CMakeLists.txt
+index 354bdd8613..e7e0c22fef 100644
+--- a/src/core/cluster_analysis/CMakeLists.txt
++++ b/src/core/cluster_analysis/CMakeLists.txt
+@@ -4,7 +4,6 @@ set(cluster_analysis_SRC
+ )
+ add_library(cluster_analysis SHARED ${cluster_analysis_SRC})
+ install(TARGETS cluster_analysis LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+-set_target_properties(cluster_analysis PROPERTIES SOVERSION ${SOVERSION})
+ set_target_properties(cluster_analysis PROPERTIES MACOSX_RPATH TRUE)
+ target_link_libraries(cluster_analysis PUBLIC EspressoCore PRIVATE EspressoConfig)
+ 
+diff --git a/src/core/io/mpiio/CMakeLists.txt b/src/core/io/mpiio/CMakeLists.txt
+index 365c58295f..7c4b0dc422 100644
+--- a/src/core/io/mpiio/CMakeLists.txt
++++ b/src/core/io/mpiio/CMakeLists.txt
+@@ -1,3 +1,4 @@
+ add_library(mpiio SHARED mpiio.cpp)
+ target_include_directories(mpiio PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+ target_link_libraries(mpiio PRIVATE EspressoConfig EspressoCore MPI::MPI_CXX)
++install(TARGETS mpiio LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+diff --git a/src/core/io/reader/CMakeLists.txt b/src/core/io/reader/CMakeLists.txt
+index 1b9ee38735..6c2de627ac 100644
+--- a/src/core/io/reader/CMakeLists.txt
++++ b/src/core/io/reader/CMakeLists.txt
+@@ -1,3 +1,4 @@
+ add_library(pdbreader SHARED readpdb.cpp)
+ target_link_libraries(pdbreader PUBLIC EspressoConfig EspressoCore pdbparser)
+ target_include_directories(pdbreader PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
++install(TARGETS pdbreader LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+diff --git a/src/core/shapes/CMakeLists.txt b/src/core/shapes/CMakeLists.txt
+index 268172df6a..c0e78aeeb5 100644
+--- a/src/core/shapes/CMakeLists.txt
++++ b/src/core/shapes/CMakeLists.txt
+@@ -13,5 +13,4 @@ set(Shapes_SRC
+ )
+ add_library(Shapes SHARED ${Shapes_SRC})
+ install(TARGETS Shapes LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+-set_target_properties(Shapes PROPERTIES SOVERSION ${SOVERSION})
+ target_link_libraries(Shapes PUBLIC EspressoConfig EspressoCore)
+diff --git a/src/pdbparser/CMakeLists.txt b/src/pdbparser/CMakeLists.txt
+index c58d79e8cb..3c4a66f1dc 100644
+--- a/src/pdbparser/CMakeLists.txt
++++ b/src/pdbparser/CMakeLists.txt
+@@ -1,5 +1,6 @@
+ add_library(pdbparser SHARED ${CMAKE_CURRENT_SOURCE_DIR}/src/PdbParser.cpp)
+ target_include_directories(pdbparser PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
++install(TARGETS pdbparser LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+ if(WITH_UNIT_TESTS)
+   add_subdirectory(unit_tests)
+ endif(WITH_UNIT_TESTS)
+diff --git a/src/python/espressomd/CMakeLists.txt b/src/python/espressomd/CMakeLists.txt
+index ebe76992da..59f2b8affc 100644
+--- a/src/python/espressomd/CMakeLists.txt
++++ b/src/python/espressomd/CMakeLists.txt
+@@ -107,6 +107,7 @@ foreach(cython_file ${cython_SRC})
+       target_link_libraries(${target} PRIVATE EspressoConfig EspressoCore EspressoScriptInterface)
+       target_include_directories(${target} SYSTEM PRIVATE ${PYTHON_INCLUDE_DIRS} ${NUMPY_INCLUDE_DIR})
+       add_dependencies(espressomd ${target})
++      install(TARGETS ${target} LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+   endif()
+ endforeach()
+ 
+@@ -124,6 +125,4 @@ foreach(auxfile ${cython_AUX})
+ endforeach(auxfile)
+ 
+ install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DESTINATION ${PYTHON_INSTDIR}
+-	PATTERN "CMakeFiles" EXCLUDE PATTERN "*.cpp" EXCLUDE
+-	PATTERN "*.cmake" EXCLUDE PATTERN "Makefile" EXCLUDE) 
+-
++	FILES_MATCHING PATTERN "*.py")
+diff --git a/src/script_interface/CMakeLists.txt b/src/script_interface/CMakeLists.txt
+index d28603f816..0a8966887f 100644
+--- a/src/script_interface/CMakeLists.txt
++++ b/src/script_interface/CMakeLists.txt
+@@ -33,7 +33,6 @@ endif()
+ 
+ add_library(EspressoScriptInterface SHARED ${EspressoScriptInterface_SRC})
+ install(TARGETS EspressoScriptInterface LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+-set_target_properties(EspressoScriptInterface PROPERTIES SOVERSION ${SOVERSION})
+ target_link_libraries(EspressoScriptInterface PRIVATE EspressoConfig PUBLIC EspressoCore Shapes cluster_analysis mpiio pdbreader)
+ if(HDF5_FOUND)
+  target_link_libraries(EspressoScriptInterface PRIVATE H5mdCore)
diff --git a/espresso.spec b/espresso.spec
index c71547e..ad3991f 100644
--- a/espresso.spec
+++ b/espresso.spec
@@ -3,8 +3,8 @@
 %global shortcommit %(c=%{commit}; echo ${c:0:7})
 
 Name:           espresso
-Version:        4.0.2
-Release:        8%{?dist}
+Version:        4.1.0
+Release:        1%{?dist}
 Summary:        Extensible Simulation Package for Research on Soft matter
 
 License:        GPLv3+
@@ -13,23 +13,23 @@ URL:            http://espressomd.org
 Source0:        https://github.com/%{name}md/%{name}/archive/%{commit}/%{name}-%{commit}.tar.gz
 %else
 Source0:       https://github.com/%{name}md/%{name}/releases/download/%{version}/%{name}-%{version}.tar.gz
-# Add missing so number to libH5mdCore
-# https://github.com/espressomd/espresso/pull/2946
-Patch0:        2946.patch
+# Fix install
+# https://github.com/espressomd/espresso/pull/3228
+Patch0:        3228.diff
+# https://github.com/espressomd/espresso/issues/3230#issuecomment-538495680
+Patch1:        mpiio.patch
 %endif
 
 
 BuildRequires:  gcc-c++
+BuildRequires:  cmake3 >= 3.4
 %if 0%{?rhel}
-BuildRequires:  cmake3 >= 3.0
 BuildRequires:  python%{python3_pkgversion}-Cython
 BuildRequires:  python%{python3_pkgversion}-setuptools
 %global cython /usr/bin/cython%{python3_version}
 # no boost-mpi* for ppc64le on epel7
 ExcludeArch:   ppc64le
 %else
-BuildRequires:  cmake >= 3.0
-%global cmake3 %{cmake}
 BuildRequires:  /usr/bin/cython
 %global cython /usr/bin/cython
 %endif
@@ -51,6 +51,7 @@ BuildRequires:  python%{python3_pkgversion}-h5py
 
 Requires:       python%{python3_pkgversion}-numpy
 Requires:       %{name}-common = %{version}-%{release}
+Obsoletes:      %{name}-devel < %{version}-%{release}
 
 %description
 ESPResSo can perform Molecular Dynamics simulations of bead-spring models
@@ -74,19 +75,6 @@ ESPResSo contains a number of advanced algorithms, e.g.
 This package contains the license file and data files shared between the
 sub-packages of %{name}.
 
-%package devel
-Summary:        Development package for  %{name} packages
-Requires:       python%{python3_pkgversion}-%{name}-openmpi = %{version}-%{release}
-Requires:       python%{python3_pkgversion}-%{name}-mpich = %{version}-%{release}
-%description devel
-ESPResSo can perform Molecular Dynamics simulations of bead-spring models
-in various ensembles ((N,V,E), (N,V,T), and (N,p,T)).
-ESPResSo contains a number of advanced algorithms, e.g.
-    * DPD thermostat (for hydrodynamics)
-    * P3M, MMM2D, MMM1D, ELC for electrostatic interactions
-    * Lattice-Boltzmann for hydrodynamics
-This package contains the development libraries of %{name}.
-
 %package -n python%{python3_pkgversion}-%{name}-openmpi
 Requires:       %{name}-common = %{version}-%{release}
 Requires:       python%{python3_pkgversion}-h5py
@@ -131,10 +119,7 @@ This package contains %{name} compiled against MPICH2.
 %else
 %setup -q -n %{name}
 %patch0 -p1
-%endif
-mkdir openmpi_build mpich_build
-%if 0%{?fedora} <= 29
-sed -i 's/1.67/1.66/' CMakeLists.txt
+%patch1 -p1
 %endif
 
 %build
@@ -149,87 +134,46 @@ sed -i 's/1.67/1.66/' CMakeLists.txt
 #save some memory using -j1
 %define _smp_mflags -j1
 
-# Build OpenMPI version
-%{_openmpi_load}
-pushd openmpi_build
-%{cmake3} \
-  %{defopts} \
-  -DLIBDIR=${MPI_LIB} \
-  -DPYTHON_INSTDIR=%{python3_sitearch}/openmpi \
-  ..
-%make_build
-popd
-%{_openmpi_unload}
-
-# Build mpich version
-%{_mpich_load}
-pushd mpich_build
-%{cmake3} \
-  %{defopts} \
-  -DLIBDIR=${MPI_LIB} \
-  -DPYTHON_INSTDIR=%{python3_sitearch}/mpich \
-  ..
-%make_build
-popd
-%{_mpich_unload}
+for mpi in mpich openmpi ; do
+   module load mpi/${mpi}-%{_arch}
+   mkdir ${mpi}
+   pushd ${mpi}
+   %{cmake3} %{defopts} -DLIBDIR=${MPI_LIB} -DPYTHON_INSTDIR=${MPI_PYTHON3_SITEARCH} ..
+   %make_build
+   popd
+   module unload mpi/${mpi}-%{_arch}
+done
 
 %install
-# first install mpi files and move around because MPI_SUFFIX above doesn't
-# work yet (will be fixed in a new version)
-%{_openmpi_load}
-pushd openmpi_build
-%make_install
-popd
-%{_openmpi_unload}
-
-%{_mpich_load}
-pushd mpich_build
-%make_install
-popd
-%{_mpich_unload}
-find %{buildroot}%{_prefix} -name "*.so" -exec chmod +x {} \;
-find %{buildroot}%{_prefix} -name "gen_pxiconfig" -exec chmod +x {} \;
+for mpi in mpich openmpi ; do
+   module load mpi/${mpi}-%{_arch}
+   %make_install -C "${mpi}"
+   module unload mpi/${mpi}-%{_arch}
+done
 
 %check
-# https://github.com/espressomd/espresso/issues/2468
-%if 0%{?fedora} <= 29
-%ifarch ppc64 ppc64le aarch64
-%global testargs ARGS='-E npt'
-%endif
-# old Boost.MPI versions contain a use-after-free bug that seems to only cause crashes on 32-bit plattform
-# remove after boost>=1.67 is available
-%ifarch i686 %arm
-%global testargs ARGS='-E .'
-%endif
-%endif
-%{_openmpi_load}
-pushd openmpi_build
-LD_LIBRARY_PATH=${MPI_LIB}:%{buildroot}${MPI_LIB} make check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}}
-popd
-%{_openmpi_unload}
-
-%{_mpich_load}
-pushd mpich_build
-LD_LIBRARY_PATH=${MPI_LIB}:%{buildroot}${MPI_LIB} make check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}}
-popd
-%{_mpich_unload}
+for mpi in mpich openmpi ; do
+   module load mpi/${mpi}-%{_arch}
+   LD_LIBRARY_PATH=${MPI_LIB}:%{buildroot}${MPI_PYTHON3_SITEARCH}/%{name}md make -C "${mpi}" check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}}
+   module unload mpi/${mpi}-%{_arch}
+done
 
 %files common
 %doc AUTHORS README NEWS ChangeLog
 %license COPYING
 
-%files devel
-%{_libdir}/*/lib/lib*.so
-
 %files -n python%{python3_pkgversion}-%{name}-openmpi
-%{_libdir}/openmpi/lib/lib*.so.*
-%{python3_sitearch}/openmpi/%{name}md
+%{python3_sitearch}/openmpi/%{name}md/
 
 %files -n python%{python3_pkgversion}-%{name}-mpich
-%{_libdir}/mpich/lib/lib*.so.*
-%{python3_sitearch}/mpich/%{name}md
+%{python3_sitearch}/mpich/%{name}md/
 
 %changelog
+* Tue Oct 01 2019 Christoph Junghans <junghans@votca.org> - 4.1.0-1
+- Version bump to v4.1.0 (bug #1757509)
+- updated 2946.patch to 3228.diff
+- major spec clean up
+
 * Wed Sep 11 2019 Christoph Junghans <junghans@votca.org> - 4.0.2-8
 - MDAnalysis is optional
 
diff --git a/mpiio.patch b/mpiio.patch
new file mode 100644
index 0000000..287ee76
--- /dev/null
+++ b/mpiio.patch
@@ -0,0 +1,11 @@
+--- espresso/src/core/io/mpiio/mpiio.cpp.orig	2019-10-04 12:17:47.025423034 -0600
++++ espresso/src/core/io/mpiio/mpiio.cpp	2019-10-04 12:18:04.708572591 -0600
+@@ -448,7 +448,7 @@
+       int blen = boff[i + 1] - boff[i];
+       auto &bl = local_particles[id[i]]->bl;
+       bl.resize(blen);
+-      std::copy_n(&bond[boff[i]], blen, bl.begin());
++      if(blen) std::copy_n(&bond[boff[i]], blen, bl.begin());
+     }
+   }
+ 
diff --git a/sources b/sources
index e91b8dd..4a5d742 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (espresso-4.0.2.tar.gz) = 0033bcc6da3129988923f5521edfcbd689871fb355a33f6b9f4d4146e2af084eb987a73466c8ba8f2553aa2617fdfb650c42a3180c5c7fa29a0cd296d48424be
+SHA512 (espresso-4.1.0.tar.gz) = 5c164118a7c2d498b2891a00528a348a5ca6ef9c1dc33b0c92b116bd91701108ec91bbc00c3eb396411c33dbfc489832afcad72b9d83daecc58392047532dfea