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 - [email protected] + +- 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 <[email protected]> # Fixed for multi-distro build by Klaus Kaempf <[email protected]> @@ -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="$DEV" \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags}" \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \ ++++++ votca-csg-1.2.3.tar.gz -> votca-csg-1.2.4.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/votca-csg-1.2.3/CMakeLists.txt new/votca-csg-1.2.4/CMakeLists.txt --- old/votca-csg-1.2.3/CMakeLists.txt 2012-08-15 06:27:37.000000000 +0200 +++ new/votca-csg-1.2.4/CMakeLists.txt 2014-08-31 23:55:07.000000000 +0200 @@ -2,7 +2,7 @@ project(votca-csg) -set(PROJECT_VERSION "1.2.3") +set(PROJECT_VERSION "1.2.4") set(PROJECT_CONTACT "[email protected]") string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\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 <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/typedefs.h> - #include <gromacs/legacyheaders/smalloc.h> - #include <gromacs/legacyheaders/vec.h> - #include <gromacs/legacyheaders/copyrite.h> - #include <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/tpxio.h> + #include <gromacs/fileio/tpxio.h> #elif GMX == 45 #include <gromacs/statutil.h> #include <gromacs/typedefs.h> @@ -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 <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/typedefs.h> - #include <gromacs/legacyheaders/smalloc.h> - #include <gromacs/legacyheaders/vec.h> - #include <gromacs/legacyheaders/copyrite.h> - #include <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/tpxio.h> + #include <gromacs/fileio/trxio.h> #elif GMX == 45 #include <gromacs/statutil.h> #include <gromacs/typedefs.h> 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 <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/typedefs.h> - #include <gromacs/legacyheaders/smalloc.h> - #include <gromacs/legacyheaders/vec.h> - #include <gromacs/legacyheaders/copyrite.h> - #include <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/tpxio.h> + #include <gromacs/fileio/trxio.h> #elif GMX == 45 #include <gromacs/statutil.h> #include <gromacs/typedefs.h> 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 <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/typedefs.h> - #include <gromacs/legacyheaders/smalloc.h> - #include <gromacs/legacyheaders/confio.h> - #include <gromacs/legacyheaders/vec.h> - #include <gromacs/legacyheaders/copyrite.h> - #include <gromacs/legacyheaders/statutil.h> - #include <gromacs/legacyheaders/tpxio.h> + #include <gromacs/fileio/trxio.h> + #include <gromacs/fileio/confio.h> + #include <gromacs/utility/smalloc.h> #elif GMX == 45 #include <gromacs/statutil.h> #include <gromacs/typedefs.h> @@ -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: [email protected] For additional commands, e-mail: [email protected]
