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Hello community,
here is the log from the commit of package votca-csg for openSUSE:Factory
checked in at 2021-07-22 22:43:34
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/votca-csg (Old)
and /work/SRC/openSUSE:Factory/.votca-csg.new.1899 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "votca-csg"
Thu Jul 22 22:43:34 2021 rev:24 rq:907763 version:2021.1
Changes:
--------
--- /work/SRC/openSUSE:Factory/votca-csg/votca-csg.changes 2021-03-17
20:19:27.951277410 +0100
+++ /work/SRC/openSUSE:Factory/.votca-csg.new.1899/votca-csg.changes
2021-07-22 22:44:30.291110310 +0200
@@ -1,0 +2,9 @@
+Sun Jul 18 14:05:45 UTC 2021 - Christoph Junghans <jungh...@votca.org>
+
+- Update to 2021.1
+ - format code with clang-12 and drop gmx2020 builds
+ ([gh#votca/csg#691])
+ - fix pos scaling (ang2nm) in lammps data reader
+ ([gh#votca/csg#697])
+
+-------------------------------------------------------------------
Old:
----
votca-csg-2021.tar.gz
votca-csg-tutorials-2021.tar.gz
New:
----
votca-csg-2021.1.tar.gz
votca-csg-tutorials-2021.1.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ votca-csg.spec ++++++
--- /var/tmp/diff_new_pack.gJXcMN/_old 2021-07-22 22:44:30.919109492 +0200
+++ /var/tmp/diff_new_pack.gJXcMN/_new 2021-07-22 22:44:30.923109487 +0200
@@ -18,7 +18,7 @@
Name: votca-csg
-Version: 2021
+Version: 2021.1
Release: 0
%define uversion %version
%define sover 2021
@@ -31,7 +31,7 @@
BuildRoot: %{_tmppath}/%{name}-%{version}-build
-BuildRequires: cmake >= 2.8.4
+BuildRequires: cmake >= 3.12
BuildRequires: fdupes
BuildRequires: gcc-c++
BuildRequires: gromacs-devel
++++++ votca-csg-2021.tar.gz -> votca-csg-2021.1.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/CHANGELOG.rst new/csg-2021.1/CHANGELOG.rst
--- old/csg-2021/CHANGELOG.rst 2021-03-13 02:24:22.000000000 +0100
+++ new/csg-2021.1/CHANGELOG.rst 2021-07-18 02:25:37.000000000 +0200
@@ -1,6 +1,12 @@
For more detailed information about the changes see the history of the
`repository <https://github.com/votca/csg/commits/master>`__.
+Version 2021.1 (released 18.07.21)
+==================================
+
+- format code with clang-12 and drop gmx2020 builds (#691)
+- fix pos scaling (ang2nm) in lammps data reader (#697)
+
Version 2021 (released 13.03.21)
================================
@@ -9,7 +15,7 @@
- namespace bind2nd to fix build on FreeBSD (#668)
- replace std::bind2nd by a lambda (#673)
-Version 2021-rc.1 (released 13.03.21)
+Version 2021-rc.1 (released 15.01.21)
=====================================
- remove topology item (#486)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/CMakeLists.txt new/csg-2021.1/CMakeLists.txt
--- old/csg-2021/CMakeLists.txt 2021-03-13 02:24:22.000000000 +0100
+++ new/csg-2021.1/CMakeLists.txt 2021-07-18 02:25:37.000000000 +0200
@@ -2,7 +2,7 @@
project(votca-csg LANGUAGES CXX)
-set(PROJECT_VERSION "2021")
+set(PROJECT_VERSION "2021.1")
string(REGEX REPLACE "[-.].*$" "" SOVERSION "${PROJECT_VERSION}")
if (NOT ${SOVERSION} MATCHES "^[0-9]+$")
message(FATAL_ERROR "Could not determine SOVERSION (${SOVERSION}) from
${PROJECT_VERSION}")
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/csgapps/orientcorr/orientcorr.cc
new/csg-2021.1/src/csgapps/orientcorr/orientcorr.cc
--- old/csg-2021/src/csgapps/orientcorr/orientcorr.cc 2021-03-13
02:24:22.000000000 +0100
+++ new/csg-2021.1/src/csgapps/orientcorr/orientcorr.cc 2021-07-18
02:25:37.000000000 +0200
@@ -115,10 +115,12 @@
"cutoff for the neighbor search")(
"nbins",
boost::program_options::value<votca::Index>(&_nbins)->default_value(40),
- "number of bins for the grid")(
- "nbmethod",
- boost::program_options::value<string>(&_nbmethod)->default_value("grid"),
- "neighbor search algorithm (simple or grid)");
+ "number of bins for the grid")("nbmethod",
+ boost::program_options::value<string>(
+ &_nbmethod)
+ ->default_value("grid"),
+ "neighbor search algorithm (simple or "
+ "grid)");
}
NBList *OrientCorrApp::CreateNBSearch() {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/csgapps/traj_force/traj_force.cc
new/csg-2021.1/src/csgapps/traj_force/traj_force.cc
--- old/csg-2021/src/csgapps/traj_force/traj_force.cc 2021-03-13
02:24:22.000000000 +0100
+++ new/csg-2021.1/src/csgapps/traj_force/traj_force.cc 2021-07-18
02:25:37.000000000 +0200
@@ -37,9 +37,14 @@
boost::program_options::value<double>(&_scale)->default_value(-1.0),
" scaling factor for trajectory forces")(
"trj-force", boost::program_options::value<string>(),
- " atomistic reference trajectory containing forces to add/subtract")(
- "out", boost::program_options::value<string>(),
- " output trajectory file with resultant forces");
+ " atomistic reference "
+ "trajectory containing forces "
+ "to add/subtract")("out", boost::program_options::value<string>(),
+ " output "
+ "trajectory "
+ "file with "
+ "resultant "
+ "forces");
}
bool TrajForce::EvaluateOptions() {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/libcsg/csgapplication.cc
new/csg-2021.1/src/libcsg/csgapplication.cc
--- old/csg-2021/src/libcsg/csgapplication.cc 2021-03-13 02:24:22.000000000
+0100
+++ new/csg-2021.1/src/libcsg/csgapplication.cc 2021-07-18 02:25:37.000000000
+0200
@@ -47,8 +47,10 @@
"cg", boost::program_options::value<std::string>(),
" coarse graining mapping and bond definitions (xml-file)")(
"map-ignore", boost::program_options::value<std::string>(),
- " list of molecules to ignore separated by ;")(
- "no-map", " disable mapping and act on original trajectory");
+ " list of molecules to ignore separated by ;")("no-map",
+ " disable mapping "
+ "and act on original
"
+ "trajectory");
} else {
AddProgramOptions("Mapping options")(
"cg", boost::program_options::value<std::string>(),
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/libcsg/modules/io/lammpsdatareader.cc
new/csg-2021.1/src/libcsg/modules/io/lammpsdatareader.cc
--- old/csg-2021/src/libcsg/modules/io/lammpsdatareader.cc 2021-03-13
02:24:22.000000000 +0100
+++ new/csg-2021.1/src/libcsg/modules/io/lammpsdatareader.cc 2021-07-18
02:25:37.000000000 +0200
@@ -496,7 +496,7 @@
}
Eigen::Vector3d xyz_pos(x, y, z);
- b->setPos(xyz_pos);
+ b->setPos(xyz_pos * tools::conv::ang2nm);
}
if (top.BeadCount() != numberOf_["atoms"]) {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/tests/test_lammpsdatareader.cc
new/csg-2021.1/src/tests/test_lammpsdatareader.cc
--- old/csg-2021/src/tests/test_lammpsdatareader.cc 2021-03-13
02:24:22.000000000 +0100
+++ new/csg-2021.1/src/tests/test_lammpsdatareader.cc 2021-07-18
02:25:37.000000000 +0200
@@ -61,12 +61,12 @@
lammpsDataReader->ReadTopology(lammpsdatafilename, top);
BOOST_CHECK_EQUAL(top.BeadCount(), 100);
- Eigen::Vector3d first_bead_correct_pos(62.806, 52.5127, 49.8873);
+ Eigen::Vector3d first_bead_correct_pos(6.2806, 5.25127, 4.98873);
Bead *firstBead = top.getBead(0);
auto first_bead_pos = firstBead->getPos();
BOOST_CHECK(first_bead_correct_pos.isApprox(first_bead_pos, 1e-3));
- Eigen::Vector3d last_bead_correct_pos(102.78495, 78.0388, 59.9629);
+ Eigen::Vector3d last_bead_correct_pos(10.278495, 7.80388, 5.99629);
Bead *lastBead = top.getBead(99);
auto last_bead_pos = lastBead->getPos();
BOOST_CHECK(last_bead_correct_pos.isApprox(last_bead_pos, 1e-3));
@@ -120,7 +120,7 @@
BOOST_CHECK_EQUAL(top.BeadCount(), 100);
- Eigen::Vector3d first_bead_correct_pos(65.7991, 51.04235, 58.480193);
+ Eigen::Vector3d first_bead_correct_pos(6.57991, 5.104235, 5.8480193);
Bead *firstBead = top.getBead(0);
auto first_bead_pos = firstBead->getPos();
@@ -128,7 +128,7 @@
cout << first_bead_pos << endl;
BOOST_CHECK(first_bead_correct_pos.isApprox(first_bead_pos, 1e-3));
- Eigen::Vector3d last_bead_correct_pos(108.431, 83.94695, 68.5254);
+ Eigen::Vector3d last_bead_correct_pos(10.8431, 8.394695, 6.85254);
Bead *lastBead = top.getBead(99);
auto last_bead_pos = lastBead->getPos();
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/tools/csg_map.cc
new/csg-2021.1/src/tools/csg_map.cc
--- old/csg-2021/src/tools/csg_map.cc 2021-03-13 02:24:22.000000000 +0100
+++ new/csg-2021.1/src/tools/csg_map.cc 2021-07-18 02:25:37.000000000 +0200
@@ -55,11 +55,19 @@
CsgApplication::Initialize();
AddProgramOptions()("out", boost::program_options::value<string>(),
" output file for coarse-grained trajectory")(
- "vel", " Write mapped velocities (if available)")(
- "force", " Write mapped forces (if available)")(
- "hybrid",
- " Create hybrid trajectory containing both atomistic and "
- "coarse-grained");
+ "vel",
+ " Write mapped velocities (if available)")("force",
+ " Write mapped forces (if
"
+ "available)")("hybrid",
+ " Create "
+ "hybrid "
+ "trajectory "
+ "containing "
+ "both "
+ "atomistic "
+ "and "
+ "coarse-"
+ "grained");
}
bool EvaluateOptions() override {
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-2021/src/tools/csg_stat.cc
new/csg-2021.1/src/tools/csg_stat.cc
--- old/csg-2021/src/tools/csg_stat.cc 2021-03-13 02:24:22.000000000 +0100
+++ new/csg-2021.1/src/tools/csg_stat.cc 2021-07-18 02:25:37.000000000
+0200
@@ -71,13 +71,26 @@
AddProgramOptions("Specific options")("options",
boost::program_options::value<string>(),
" options file for coarse graining")(
- "do-imc", " write out additional Inverse Monte Carlo data")(
- "block-length", boost::program_options::value<votca::Index>(),
- " write blocks of this length, the averages are cleared after every "
- "write")("ext",
- boost::program_options::value<string>(&_extension)
- ->default_value("dist.new"),
- "Extension of the output");
+ "do-imc",
+ " write out additional Inverse Monte Carlo data")("block-length",
+
boost::program_options::
+ value<votca::
+
Index>(),
+ " write blocks of "
+ "this length, the "
+ "averages are cleared
"
+ "after every "
+ "write")("ext",
+
boost::program_options::value<
+ string>(
+
&_extension)
+
->default_value(
+
"dist"
+ ".ne"
+ "w"),
+ "Extension "
+ "of the "
+ "output");
}
bool CsgStatApp::EvaluateOptions() {
++++++ votca-csg-tutorials-2021.tar.gz -> votca-csg-tutorials-2021.1.tar.gz
++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/csg-tutorials-2021/CMakeLists.txt
new/csg-tutorials-2021.1/CMakeLists.txt
--- old/csg-tutorials-2021/CMakeLists.txt 2021-03-13 02:24:23.000000000
+0100
+++ new/csg-tutorials-2021.1/CMakeLists.txt 2021-07-18 02:25:38.000000000
+0200
@@ -2,7 +2,7 @@
project(csg-tutorials LANGUAGES NONE)
-set(PROJECT_VERSION "2021")
+set(PROJECT_VERSION "2021.1")
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules)
