Hello community,
here is the log from the commit of package votca-csg for openSUSE:Factory checked in at 2014-09-07 11:10:08
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/votca-csg (Old)
and /work/SRC/openSUSE:Factory/.votca-csg.new (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "votca-csg"
Changes:
--------
--- /work/SRC/openSUSE:Factory/votca-csg/votca-csg.changes 2014-02-22 18:17:42.000000000 +0100
+++ /work/SRC/openSUSE:Factory/.votca-csg.new/votca-csg.changes 2014-09-07 11:10:14.000000000 +0200
@@ -1,0 +2,6 @@
+Fri Sep 5 22:00:07 UTC 2014 - junghans@votca.org
+
+- Update to 1.2.4
+ - support for Gromacs 5.0
+
+-------------------------------------------------------------------
Old:
----
votca-csg-1.2.3.tar.gz
votca-csg-manual-1.2.3.pdf
votca-csg-tutorials-1.2.3.tar.gz
New:
----
votca-csg-1.2.4.tar.gz
votca-csg-manual-1.2.4.pdf
votca-csg-tutorials-1.2.4.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ votca-csg.spec ++++++
--- /var/tmp/diff_new_pack.EA6ngx/_old 2014-09-07 11:10:16.000000000 +0200
+++ /var/tmp/diff_new_pack.EA6ngx/_new 2014-09-07 11:10:16.000000000 +0200
@@ -1,7 +1,7 @@
#
# votca-csg.spec
#
-# Copyright (c) 2013,2014 Christoph Junghans
+# Copyright (c) 2013-2014 Christoph Junghans
#
# Originally written by Jussi Lehtola
# Fixed for multi-distro build by Klaus Kaempf
@@ -10,15 +10,15 @@
#
Name: votca-csg
-Version: 1.2.3
+Version: 1.2.4
Release: 0
Summary: VOTCA coarse-graining engine
Group: Productivity/Scientific/Chemistry
License: Apache-2.0
URL: http://www.votca.org
-Source0: http://votca.googlecode.com/files/%{name}-%{version}.tar.gz
-Source1: http://votca.googlecode.com/files/%{name}-tutorials-%{version}.tar.gz
-Source2: http://votca.googlecode.com/files/%{name}-manual-%{version}.pdf
+Source0: http://downloads.votca.googlecode.com/hg/%{name}-%{version}.tar.gz
+Source1: http://downloads.votca.googlecode.com/hg/%{name}-tutorials-%{version}.tar.gz
+Source2: http://downloads.votca.googlecode.com/hg/%{name}-manual-%{version}.pdf
BuildRoot: %{_tmppath}/%{name}-%{version}-build
@@ -116,6 +116,7 @@
rm -rf %{name}-tutorials-%{version}/.hg*
%build
+pkg-config libgromacs && DEV=ON || DEV=OFF
%if %{defined fedora}
mkdir build
cd build
@@ -125,8 +126,10 @@
mkdir build
cd build
%endif
-%{cmake} -DCMAKE_INSTALL_PREFIX=/usr \
+%{cmake} \
+ -DCMAKE_INSTALL_PREFIX=%{_prefix} \
-DWITH_RC_FILES=OFF \
+ -DWITH_GMX_DEVEL="$DEV" \
-DCMAKE_VERBOSE_MAKEFILE=TRUE \
-DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags}" \
-DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \
++++++ votca-csg-1.2.3.tar.gz -> votca-csg-1.2.4.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/CMakeLists.txt new/votca-csg-1.2.4/CMakeLists.txt
--- old/votca-csg-1.2.3/CMakeLists.txt 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/CMakeLists.txt 2014-08-31 23:55:07.000000000 +0200
@@ -2,7 +2,7 @@
project(votca-csg)
-set(PROJECT_VERSION "1.2.3")
+set(PROJECT_VERSION "1.2.4")
set(PROJECT_CONTACT "bugs@votca.org")
string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}")
if (NOT ${SOVERSION} MATCHES "[1-9]+")
@@ -46,6 +46,8 @@
########################################################################
#Find external packages
########################################################################
+find_package(Threads REQUIRED)
+set(THREAD_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
find_package(TXT2TAGS)
option(EXTERNAL_BOOST "Use external boost" ON)
if (EXTERNAL_BOOST)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/CMakeModules/FindGROMACS.cmake new/votca-csg-1.2.4/CMakeModules/FindGROMACS.cmake
--- old/votca-csg-1.2.3/CMakeModules/FindGROMACS.cmake 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/CMakeModules/FindGROMACS.cmake 2014-08-31 23:55:07.000000000 +0200
@@ -30,70 +30,54 @@
elseif(${GROMACS_NUM_COMPONENTS_WANTED} GREATER 1)
message(FATAL_ERROR "We only support finding one gromacs component at this point, go and implement it ;-)")
elseif(${GROMACS_FIND_COMPONENTS} MATCHES "^lib(gmx|gromacs)(_d)?$")
- set(GROMACS_PKG "${GROMACS_FIND_COMPONENTS}")
+ if(NOT GROMACS_PKG_OVERWRITE)
+ set(GROMACS_PKG "${GROMACS_FIND_COMPONENTS}")
+ else()
+ set(GROMACS_PKG "${GROMACS_PKG_OVERWRITE}")
+ endif()
string(REGEX REPLACE "^lib(.*)" "\\1" GROMACS_LIBRARY_NAME "${GROMACS_PKG}")
else()
message(FATAL_ERROR "We do not support finding ${GROMACS_FIND_COMPONENTS}, go and implement it ;-)")
endif()
-if(GMX_DOUBLE AND NOT "${GROMACS_PKG}" MATCHES "_d$")
- message(FATAL_ERROR "GMX_DOUBLE was true, but I was asked to find ${GROMACS_PKG} (without _d at the end) - unlogical!")
-endif(GMX_DOUBLE AND NOT "${GROMACS_PKG}" MATCHES "_d$")
-
pkg_check_modules(PC_GROMACS ${GROMACS_PKG})
-if (GMX_DOUBLE)
- list(APPEND GMX_DEFS "-DGMX_DOUBLE")
-endif(GMX_DOUBLE)
-if (PC_GROMACS_CFLAGS_OTHER)
- foreach(DEF ${PC_GROMACS_CFLAGS_OTHER})
- if (${DEF} MATCHES "^-D")
- list(APPEND GMX_DEFS ${DEF})
- endif (${DEF} MATCHES "^-D")
- endforeach(DEF)
- list(REMOVE_DUPLICATES GMX_DEFS)
-endif (PC_GROMACS_CFLAGS_OTHER)
-set(GROMACS_DEFINITIONS "${GMX_DEFS}" CACHE STRING "extra GROMACS definitions")
find_library(GROMACS_LIBRARY NAMES ${GROMACS_LIBRARY_NAME} HINTS ${PC_GROMACS_LIBRARY_DIRS} )
if (GROMACS_LIBRARY)
- if("${GROMACS_LIBRARY}" MATCHES "lib(gmx|gromacs)[^;]*\\.a")
- if(PC_GROMACS_LIBRARIES)
- list(REMOVE_ITEM PC_GROMACS_LIBRARIES ${GROMACS_LIBRARY_NAME})
- foreach (LIB ${PC_GROMACS_LIBRARIES})
- find_library(GROMACS_${LIB} NAMES ${LIB} HINTS ${PC_GROMACS_LIBRARY_DIRS} )
- list(APPEND GMX_DEP_LIBRARIES ${GROMACS_${LIB}})
- unset(GROMACS_${LIB} CACHE)
- endforeach(LIB)
- endif(PC_GROMACS_LIBRARIES)
- if(PC_GROMACS_CFLAGS_OTHER)
- foreach(LIB ${PC_GROMACS_CFLAGS_OTHER})
- if (${LIB} MATCHES "thread")
- find_package(Threads REQUIRED)
- list(APPEND GMX_DEP_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
- endif (${LIB} MATCHES "thread")
- endforeach(LIB)
- endif(PC_GROMACS_CFLAGS_OTHER)
- set(GROMACS_DEP_LIBRARIES "${GMX_DEP_LIBRARIES}" CACHE FILEPATH "gromacs depency libs (only needed for static (.a) libgmx")
- endif("${GROMACS_LIBRARY}" MATCHES "lib(gmx|gromacs)[^;]*\\.a")
include(CheckLibraryExists)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" GromacsVersion "" FOUND_GROMACS_VERSION)
+ check_library_exists("${GROMACS_LIBRARY}" GromacsVersion "" FOUND_GROMACS_VERSION)
if(NOT FOUND_GROMACS_VERSION)
- message(FATAL_ERROR "Could not find GromacsVersion in ${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. If you don't have pkg-config installed you will most likely have to set GROMACS_LIBRARY and GROMACS_DEP_LIBRARY by hand which sets the gromacs lib and it's depencies (i.e. -DGROMACS_LIBRARY='/path/to/libgmx.so' -DGROMACS_DEP_LIBRARIES='/path/to/libblas.so;/path/to/libm.so') !")
+ message(FATAL_ERROR "Could not find GromacsVersion in ${GROMACS_LIBRARY}, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. If you don't have pkg-config installed you will most likely have to set GROMACS_LIBRARY by hand which sets the gromacs lib and it's dependencies (i.e. -DGROMACS_LIBRARY='/path/to/libgmx.so;/path/to/libblas.so;/path/to/libm.so')!")
endif(NOT FOUND_GROMACS_VERSION)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" init_mtop "" FOUND_GROMACS_INIT_MTOP)
+ check_library_exists("${GROMACS_LIBRARY}" init_mtop "" FOUND_GROMACS_INIT_MTOP)
if(NOT FOUND_GROMACS_INIT_MTOP)
message(FATAL_ERROR "Could not find init_mtop in the gromacs library, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. This most likely means that your gromacs version is too old, we need at least gromacs 4.0.7.")
endif(NOT FOUND_GROMACS_INIT_MTOP)
set(GMX_VERSION 40)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" output_env_init "" FOUND_GROMACS_OUTPUT_ENV_INIT)
+ check_library_exists("${GROMACS_LIBRARY}" output_env_init "" FOUND_GROMACS_OUTPUT_ENV_INIT)
if(FOUND_GROMACS_OUTPUT_ENV_INIT)
set(GMX_VERSION 45)
endif(FOUND_GROMACS_OUTPUT_ENV_INIT)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" init_domdec_vsites "" FOUND_GROMACS_INIT_DOMDEC_VSITES)
+ check_library_exists("${GROMACS_LIBRARY}" init_domdec_vsites "" FOUND_GROMACS_INIT_DOMDEC_VSITES)
if(FOUND_GROMACS_INIT_DOMDEC_VSITES)
set(GMX_VERSION 50)
endif(FOUND_GROMACS_INIT_DOMDEC_VSITES)
- set(GROMACS_VERSION ${GMX_VERSION} CACHE STRING "Gromacs lib interface version")
+ set(GROMACS_VERSION ${GMX_VERSION})
+
+ #Only set GROMACS_DEFINITIONS if GROMACS_LIBRARY was found
+ if ("${GROMACS_LIBRARY}" MATCHES "lib[^/]*_d\\.[^.]*$")
+ list(APPEND GMX_DEFS "-DGMX_DOUBLE")
+ endif ("${GROMACS_LIBRARY}" MATCHES "lib[^/]*_d\\.[^.]*$")
+ if (PC_GROMACS_CFLAGS_OTHER)
+ foreach(DEF ${PC_GROMACS_CFLAGS_OTHER})
+ if (${DEF} MATCHES "^-D")
+ list(APPEND GMX_DEFS ${DEF})
+ endif (${DEF} MATCHES "^-D")
+ endforeach(DEF)
+ list(REMOVE_DUPLICATES GMX_DEFS)
+ endif (PC_GROMACS_CFLAGS_OTHER)
+ set(GROMACS_DEFINITIONS "${GMX_DEFS}")
+
else(GROMACS_LIBRARY)
set(GMX_VERSION 45)
endif (GROMACS_LIBRARY)
@@ -105,10 +89,10 @@
find_path(GROMACS_INCLUDE_DIR gromacs/tpxio.h HINTS ${PC_GROMACS_INCLUDE_DIRS})
endif(${GMX_VERSION} EQUAL 40)
elseif("${GROMACS_PKG}" MATCHES "libgromacs")
- find_path(GROMACS_INCLUDE_DIR gromacs/legacyheaders/tpxio.h HINTS ${PC_GROMACS_INCLUDE_DIRS})
+ find_path(GROMACS_INCLUDE_DIR gromacs/fileio/tpxio.h HINTS ${PC_GROMACS_INCLUDE_DIRS})
endif("${GROMACS_PKG}" MATCHES "libgmx")
-set(GROMACS_LIBRARIES "${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" )
+set(GROMACS_LIBRARIES "${GROMACS_LIBRARY}" )
set(GROMACS_INCLUDE_DIRS ${GROMACS_INCLUDE_DIR} )
include(FindPackageHandleStandardArgs)
@@ -116,4 +100,4 @@
# if all listed variables are TRUE
find_package_handle_standard_args(GROMACS DEFAULT_MSG GROMACS_LIBRARY GROMACS_INCLUDE_DIR)
-mark_as_advanced(GROMACS_INCLUDE_DIR GROMACS_LIBRARY GROMACS_DEFINITIONS GROMACS_PKG GROMACS_VERSION GROMACS_DEP_LIBRARIES)
+mark_as_advanced(GROMACS_INCLUDE_DIR GROMACS_LIBRARY GROMACS_PKG)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/CMakeModules/FindVOTCA_TOOLS.cmake new/votca-csg-1.2.4/CMakeModules/FindVOTCA_TOOLS.cmake
--- old/votca-csg-1.2.3/CMakeModules/FindVOTCA_TOOLS.cmake 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/CMakeModules/FindVOTCA_TOOLS.cmake 2014-08-31 23:55:07.000000000 +0200
@@ -54,7 +54,7 @@
include(CheckLibraryExists)
check_library_exists("${VOTCA_TOOLS_LIBRARY};${VOTCA_TOOLS_DEP_LIBRARIES}" VotcaToolsFromC "" FOUND_VOTCA_TOOLS_VERSION)
if(NOT FOUND_VOTCA_TOOLS_VERSION)
- message(FATAL_ERROR "Could not find VotcaToolsFromC in ${VOTCA_TOOLS_LIBRARY};${VOTCA_TOOLS_DEP_LIBRARIES}, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. If you don't have pkg-config installed you will most likely have to set VOTCA_TOOLS_LIBRARY and VOTCA_TOOLS_DEP_LIBRARIES by hand, which set votca_tools lib it's depencies (i.e. -DVOTCA_TOOLS_LIBRARY='/path/to/libvotca_tools.so" -VOTCA_TOOLS_DEP_LIBRARIES="/path/to/libgsl.so;/path/to/libm.so') !")
+ message(FATAL_ERROR "Could not find VotcaToolsFromC in ${VOTCA_TOOLS_LIBRARY};${VOTCA_TOOLS_DEP_LIBRARIES}, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. If you don't have pkg-config installed you will most likely have to set VOTCA_TOOLS_LIBRARY and VOTCA_TOOLS_DEP_LIBRARIES by hand, which set votca_tools lib it's depencies (i.e. -DVOTCA_TOOLS_LIBRARY='/path/to/libvotca_tools.so' -DVOTCA_TOOLS_DEP_LIBRARIES='/path/to/libgsl.so;/path/to/libm.so') !")
endif(NOT FOUND_VOTCA_TOOLS_VERSION)
endif (VOTCA_TOOLS_FOUND)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/ChangeLog new/votca-csg-1.2.4/ChangeLog
--- old/votca-csg-1.2.3/ChangeLog 2012-08-15 06:27:39.000000000 +0200
+++ new/votca-csg-1.2.4/ChangeLog 2014-08-31 23:55:08.000000000 +0200
@@ -1,3 +1,12 @@
+Version 1.2.4 (released 31.08.14)
+
+* support for Gromacs 5.0
+* support for Boost 1.53
+* fixed use of nawk instead of gawk under MacOs
+* fixed python shebang
+* fixed linking issue under Fedora
+* fixed thermforce calculation for xsplit case
+
Version 1.2.3 (released 14.08.12)
* improved AIX support
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/scripts/multi_g_rdf.in new/votca-csg-1.2.4/scripts/multi_g_rdf.in
--- old/votca-csg-1.2.3/scripts/multi_g_rdf.in 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/scripts/multi_g_rdf.in 2014-08-31 23:55:07.000000000 +0200
@@ -98,7 +98,7 @@
case $1 in
-[0-9]* | --[0-9]**)
np=${1#-}
- np=${1#-}
+ np=${np#-}
[ -z "${np//[0-9]}" ] || die "$1 could not be convert to a number"
shift ;;
-b)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/RDF_to_POT.pl new/votca-csg-1.2.4/share/scripts/inverse/RDF_to_POT.pl
--- old/votca-csg-1.2.3/share/scripts/inverse/RDF_to_POT.pl 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/RDF_to_POT.pl 2014-08-31 23:55:07.000000000 +0200
@@ -76,6 +76,7 @@
last;
}
}
+die "All data points from file '$infile' are invalid after Boltzmann inversion, please check if your distribution is a valid rdf.\n" if ($first_undef_bin==$#pot);
#find i which is the cutoff
my $i_cut=$#r;
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/calc_thermforce.sh new/votca-csg-1.2.4/share/scripts/inverse/calc_thermforce.sh
--- old/votca-csg-1.2.3/share/scripts/inverse/calc_thermforce.sh 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/calc_thermforce.sh 2014-08-31 23:55:07.000000000 +0200
@@ -45,7 +45,7 @@
else
outfile="${name}.sym.dens"
adressc="$(get_simulation_setting adress_reference_coords "0")"
- ref="$(echo "$adressc" | awk '{if (NF<1) exit 1; print "$1";}')" || die "${0##*/}: we need at least one number in adress_reference_coords, but got '$adressc'"
+ ref="$(echo "$adressc" | awk '{if (NF<1) exit 1; print $1;}')" || die "${0##*/}: we need at least one number in adress_reference_coords, but got '$adressc'"
critical do_external density symmetrize --infile "$infile" --outfile "$outfile" --adressc "$ref"
infile="${outfile}"
fi
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/density_symmetrize.py new/votca-csg-1.2.4/share/scripts/inverse/density_symmetrize.py
--- old/votca-csg-1.2.3/share/scripts/inverse/density_symmetrize.py 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/density_symmetrize.py 2014-08-31 23:55:07.000000000 +0200
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/functions_common.sh new/votca-csg-1.2.4/share/scripts/inverse/functions_common.sh
--- old/votca-csg-1.2.3/share/scripts/inverse/functions_common.sh 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/functions_common.sh 2014-08-31 23:55:07.000000000 +0200
@@ -273,7 +273,7 @@
num_check() { #checks if 1st argument is a number or calls die with error message (2nd argument)
local res
[[ -n $1 || -n $2 ]] || die "num_check: Missing argument"
- res=$(awk -v x="$1" 'BEGIN{ print x+0==x; }')
+ res=$(awk -v x="$1" 'BEGIN{ print ( x+0==x ) }')
[[ $res -eq 1 ]] && return 0
shift
die "$*"
@@ -519,8 +519,8 @@
[[ -n "$(type -p awk)" ]] || die "csg_calc: Could not find awk"
#we use awk -v because then " 1 " or "1\n" is equal to 1
case "$2" in
- "+"|"-"|'*'|"/"|"**")
- res="$(awk -v x="$1" -v y="$3" "BEGIN{print x $2 y}")" || die "csg_calc: awk -v x='$1' -v y='$3' 'BEGIN{print x $2 y}' failed"
+ "+"|"-"|'*'|"/"|"^")
+ res="$(awk -v x="$1" -v y="$3" "BEGIN{print ( x $2 y ) }")" || die "csg_calc: awk -v x='$1' -v y='$3' 'BEGIN{print ( x $2 y ) }' failed"
true;;
'>'|'<' )
res="$(awk -v x="$1" -v y="$3" "BEGIN{print ( x $2 y )}")" || die "csg_calc: awk -v x='$1' -v y='$3' 'BEGIN{print ( x $2 y )}' failed"
@@ -531,7 +531,7 @@
true;;
"="|"==")
#we expect that x and y are close together
- res="$(awk -v x="$1" -v y="$3" "BEGIN{print ( sqrt(((x-y)/x)**2) < $err )}")" || die "csg_calc: awk -v x='$1' -v y='$3' 'BEGIN{print ( sqrt(((x-y)/x)**2) < $err )}' failed"
+ res="$(awk -v x="$1" -v y="$3" "BEGIN{print ( sqrt(((x-y)/x)^2) < $err )}")" || die "csg_calc: awk -v x='$1' -v y='$3' 'BEGIN{print ( sqrt(((x-y)/x)^2) < $err )}' failed"
#awk return 1 for true and 0 for false, shell exit codes are the other way around
ret="$((1-$res))"
#return value matters
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/linsolve.py new/votca-csg-1.2.4/share/scripts/inverse/linsolve.py
--- old/votca-csg-1.2.3/share/scripts/inverse/linsolve.py 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/linsolve.py 2014-08-31 23:55:07.000000000 +0200
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
import numpy as np
A = np.loadtxt('$name.gmc');
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/postadd_convergence.sh new/votca-csg-1.2.4/share/scripts/inverse/postadd_convergence.sh
--- old/votca-csg-1.2.3/share/scripts/inverse/postadd_convergence.sh 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/postadd_convergence.sh 2014-08-31 23:55:07.000000000 +0200
@@ -71,7 +71,7 @@
critical paste $tmp1 $tmp3 > $tmp4
critical awk '{if ($4!=$1){print "x column differs in line",NR;exit 1;}}' $tmp4
echo "Calc convergence for ${name} with weight $weight"
- critical awk -v bin=$step -v w=$weight -v dist=$dist '{sum+=($5-$2)**2;}END{print dist,sqrt(sum*bin*w);}' $tmp4 >> $tmp
+ critical awk -v bin=$step -v w=$weight -v dist=$dist '{sum+=($5-$2)^2;}END{print dist,sqrt(sum*bin*w);}' $tmp4 >> $tmp
done
critical awk '{sum+=$2;}END{print sum;}' $tmp > ${name}.conv
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/solve_numpy.sh new/votca-csg-1.2.4/share/scripts/inverse/solve_numpy.sh
--- old/votca-csg-1.2.3/share/scripts/inverse/solve_numpy.sh 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/solve_numpy.sh 2014-08-31 23:55:07.000000000 +0200
@@ -33,7 +33,7 @@
cat_external solve numpy | sed -e "s/\$name_out/$2/" -e "s/\$name/$1/" > solve_$1.sh || die "${0##*/}: sed failed"
#this check is not sufficient for numpy! check for numpy package!
-py="$(csg_get_property cg.inverse.imc.numpy.bin "python")"
+py="$(csg_get_property cg.inverse.imc.numpy.bin "python2")"
[ -n "$(type -p $py)" ] || die "${0##*/}: python binary '$py' not found"
critical $py solve_$1.sh
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/table_getsubset.py new/votca-csg-1.2.4/share/scripts/inverse/table_getsubset.py
--- old/votca-csg-1.2.3/share/scripts/inverse/table_getsubset.py 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/table_getsubset.py 2014-08-31 23:55:07.000000000 +0200
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/share/scripts/inverse/table_smooth_borders.py new/votca-csg-1.2.4/share/scripts/inverse/table_smooth_borders.py
--- old/votca-csg-1.2.3/share/scripts/inverse/table_smooth_borders.py 2012-08-15 06:27:37.000000000 +0200
+++ new/votca-csg-1.2.4/share/scripts/inverse/table_smooth_borders.py 2014-08-31 23:55:07.000000000 +0200
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/csg_boltzmann/tabulatedpotential.cc new/votca-csg-1.2.4/src/csg_boltzmann/tabulatedpotential.cc
--- old/votca-csg-1.2.3/src/csg_boltzmann/tabulatedpotential.cc 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/csg_boltzmann/tabulatedpotential.cc 2014-08-31 23:55:07.000000000 +0200
@@ -99,7 +99,7 @@
if(args.size() == 1) {
cout << cmd << " set <option> <value>\n"
<< "set option for this command. Use \"" << cmd << " set\""
- " for a list of availale options. To get telp on a specific option use e.g.\n"
+ " for a list of available options. To get help on a specific option use e.g.\n"
<< cmd << " set periodic\n";
return;
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/CMakeLists.txt new/votca-csg-1.2.4/src/libcsg/CMakeLists.txt
--- old/votca-csg-1.2.3/src/libcsg/CMakeLists.txt 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/CMakeLists.txt 2014-08-31 23:55:07.000000000 +0200
@@ -49,7 +49,7 @@
add_library(votca_csg ${VOTCA_SOURCES} ${GMX_SOURCES} ${IO_SOURCES})
add_dependencies(votca_csg hgversion)
set_target_properties(votca_csg PROPERTIES SOVERSION ${SOVERSION})
-target_link_libraries(votca_csg ${VOTCA_TOOLS_LIBRARIES} ${GROMACS_LIBRARIES} ${BOOST_LIBRARIES})
+target_link_libraries(votca_csg ${VOTCA_TOOLS_LIBRARIES} ${GROMACS_LIBRARIES} ${BOOST_LIBRARIES} ${THREAD_LIBRARIES})
install(TARGETS votca_csg LIBRARY DESTINATION ${LIB} ARCHIVE DESTINATION ${LIB})
configure_file(libvotca_csg.pc.in ${CMAKE_CURRENT_BINARY_DIR}/libvotca_csg.pc @ONLY)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/libvotca_csg.pc.in new/votca-csg-1.2.4/src/libcsg/libvotca_csg.pc.in
--- old/votca-csg-1.2.3/src/libcsg/libvotca_csg.pc.in 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/libvotca_csg.pc.in 2014-08-31 23:55:07.000000000 +0200
@@ -7,6 +7,6 @@
URL: http://www.votca.org
Version: @VERSION@
Requires: libvotca_tools @GROMACS_PKG@ @BOOST_PKG@
-Libs: -L${libdir} -lvotca_csg @BOOST_LIBS_PKG@
+Libs: -L${libdir} -lvotca_csg @BOOST_LIBS_PKG@ @THREAD_LIBRARIES@
Libs.private: -lm
Cflags: -I${includedir} @BOOST_CFLAGS_PKG@
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtopologyreader.cc new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtopologyreader.cc
--- old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtopologyreader.cc 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtopologyreader.cc 2014-08-31 23:55:07.000000000 +0200
@@ -23,13 +23,7 @@
#include "gmxtopologyreader.h"
#if GMX == 50
- #include
- #include
- #include
- #include
- #include
- #include
- #include
+ #include
#elif GMX == 45
#include
#include
@@ -64,7 +58,6 @@
int natoms;
// cleanup topology to store new data
top.Cleanup();
- set_program_name("VOTCA");
#if GMX == 50
t_inputrec ir;
@@ -72,10 +65,14 @@
(void)read_tpx((char *)file.c_str(),&ir,gbox,&natoms,NULL,NULL,NULL,&mtop);
#elif GMX == 45
+ set_program_name("VOTCA");
+
t_inputrec ir;
::matrix gbox;
(void)read_tpx((char *)file.c_str(),&ir,gbox,&natoms,NULL,NULL,NULL,&mtop);
#elif GMX == 40
+ set_program_name("VOTCA");
+
int sss; // wtf is this
::real ttt,lll; // wtf is this
(void)read_tpx((char *)file.c_str(),&sss,&ttt,&lll,NULL,NULL,&natoms,NULL,NULL,NULL,&mtop);
@@ -152,6 +149,14 @@
}
}
+#if GMX != 40
+ matrix m;
+ for(int i=0; i<3; i++)
+ for(int j=0; j<3; j++)
+ m[i][j] = gbox[j][i];
+ top.setBox(m);
+#endif
+
return true;
}
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectoryreader.cc new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectoryreader.cc
--- old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectoryreader.cc 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectoryreader.cc 2014-08-31 23:55:07.000000000 +0200
@@ -37,20 +37,20 @@
bool GMXTrajectoryReader::FirstFrame(Topology &conf)
{
- set_program_name("VOTCA");
-
#if GMX == 50
output_env_t oenv;
// _snew("oenv", oenv, 1);
- oenv = (output_env_t)malloc(sizeof(*oenv));
- output_env_init_default (oenv);
+ //oenv = (output_env_t)malloc(sizeof(*oenv));
+ output_env_init_default (&oenv);
if(!read_first_frame(oenv, &_gmx_status,(char*)_filename.c_str(),&_gmx_frame,TRX_READ_X | TRX_READ_V | TRX_READ_F))
throw std::runtime_error(string("cannot open ") + _filename);
//sfree(oenv);
free(oenv);
#elif GMX == 45
+ set_program_name("VOTCA");
+
output_env_t oenv;
// _snew("oenv", oenv, 1);
oenv = (output_env_t)malloc(sizeof(*oenv));
@@ -61,6 +61,8 @@
//sfree(oenv);
free(oenv);
#elif GMX == 40
+ set_program_name("VOTCA");
+
if(!read_first_frame(&_gmx_status,(char*)_filename.c_str(),&_gmx_frame,TRX_READ_X | TRX_READ_V | TRX_READ_F))
throw std::runtime_error(string("cannot open ") + _filename);
#else
@@ -102,8 +104,8 @@
#if GMX == 50
output_env_t oenv;
//_snew("oenv", oenv, 1);
- oenv = (output_env_t)malloc(sizeof(*oenv));
- output_env_init_default (oenv);
+ //oenv = (output_env_t)malloc(sizeof(*oenv));
+ output_env_init_default (&oenv);
if(!read_next_frame(oenv, _gmx_status,&_gmx_frame))
return false;
//sfree(oenv);
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectoryreader.h new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectoryreader.h
--- old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectoryreader.h 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectoryreader.h 2014-08-31 23:55:07.000000000 +0200
@@ -27,13 +27,7 @@
#include "gmx_version_check.h"
#if GMX == 50
- #include
- #include
- #include
- #include
- #include
- #include
- #include
+ #include
#elif GMX == 45
#include
#include
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectorywriter.cc new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectorywriter.cc
--- old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectorywriter.cc 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectorywriter.cc 2014-08-31 23:55:07.000000000 +0200
@@ -23,7 +23,9 @@
void GMXTrajectoryWriter::Open(string file, bool bAppend)
{
+#if GMX != 50
set_program_name("VOTCA");
+#endif
//char c[1] = bAppend ? "a" : "w";
_file = open_trx((char *)file.c_str(), "w");
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectorywriter.h new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectorywriter.h
--- old/votca-csg-1.2.3/src/libcsg/modules/io/gmxtrajectorywriter.h 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/gmxtrajectorywriter.h 2014-08-31 23:55:07.000000000 +0200
@@ -27,13 +27,7 @@
#include "gmx_version_check.h"
#if GMX == 50
- #include
- #include
- #include
- #include
- #include
- #include
- #include
+ #include
#elif GMX == 45
#include
#include
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/pdbtopologyreader.cc new/votca-csg-1.2.4/src/libcsg/modules/io/pdbtopologyreader.cc
--- old/votca-csg-1.2.3/src/libcsg/modules/io/pdbtopologyreader.cc 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/pdbtopologyreader.cc 2014-08-31 23:55:07.000000000 +0200
@@ -23,14 +23,9 @@
#include "pdbtopologyreader.h"
#if GMX == 50
- #include
- #include
- #include
- #include
- #include
- #include
- #include
- #include
+ #include
+ #include
+ #include
#elif GMX == 45
#include
#include
@@ -70,7 +65,9 @@
::matrix box;
int ePBC;
t_atoms atoms;
+#if GMX != 50
set_program_name("VOTCA");
+#endif
//snew(atoms,1);
get_stx_coordnum((char*)file.c_str(),&(atoms.nr));
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/src/libcsg/modules/io/xyzwriter.cc new/votca-csg-1.2.4/src/libcsg/modules/io/xyzwriter.cc
--- old/votca-csg-1.2.3/src/libcsg/modules/io/xyzwriter.cc 2012-08-15 06:27:38.000000000 +0200
+++ new/votca-csg-1.2.4/src/libcsg/modules/io/xyzwriter.cc 2014-08-31 23:55:07.000000000 +0200
@@ -37,7 +37,7 @@
void XYZWriter::Write(Topology *conf)
{
Topology *top = conf;
- fprintf(_out, "%d\n", top->Beads().size());
+ fprintf(_out, "%lu\n", top->Beads().size());
fprintf(_out, "frame: %d time: %f\n", top->getStep()+1, top->getTime());
for(BeadContainer::iterator iter=conf->Beads().begin();
++++++ votca-csg-manual-1.2.3.pdf -> votca-csg-manual-1.2.4.pdf ++++++
(binary differes)
++++++ votca-csg-tutorials-1.2.3.tar.gz -> votca-csg-tutorials-1.2.4.tar.gz ++++++
++++ 8034 lines of diff (skipped)
--
To unsubscribe, e-mail: opensuse-commit+unsubscribe@opensuse.org
For additional commands, e-mail: opensuse-commit+help@opensuse.org