Merge branch 'v2.10'

Author: GiovanniBussi

.ci/install.cppcheck

@@ -5,25 +5,31 @@ set -x
 
 cd "$(mktemp -dt plumed.XXXXXX)"
 
-git clone https://github.com/danmar/cppcheck.git
-cd cppcheck
+repo=https://github.com/danmar/cppcheck.git
 
-if [ -n "$1" ] ; then
-  echo "installing cppcheck $version"
+if [ -n "$1" ]; then
   version=$1
+  echo "installing cppcheck $version"
 else
-  echo "installing latest doxygen"
-  version=$(git tag | tail -n 1)
+  # getting the latest version without downloading the repo
+  version=$(
+    git -c 'versionsort.suffix=-' \
+      ls-remote --exit-code --refs --sort='version:refname' --tags "$repo" '*.*.*' \
+      | tail --lines=1 \
+      | cut --delimiter='/' --fields=3
+  )
+  echo "installing latest cppcheck ($version)"
 fi
 
+#cloning ONLY the code we need
+git clone "$repo" --branch "$version" --depth 1
+cd cppcheck
 # pick native architecture
 native="$($CC -march=native -Q --help=target | grep "^ *\-march" | awk '{print $2}' | head -n 1)"
 # this is required so that when running the job on a different architecture ccache understand
 # the object file should not be recycled
 
-git checkout $version
 make -j 4 install MATCHCOMPILER=yes FILESDIR="$HOME/opt/share/cppcheck" HAVE_RULES=yes CXXFLAGS="-DNDEBUG -O2 -march=$native -mtune=$native -Wall -Wno-sign-compare -Wno-unused-function" PREFIX="$HOME/opt"
 cd ../
 
 cppcheck --version
-

.ci/install.doxygen

@@ -5,19 +5,25 @@ set -x
 
 cd "$(mktemp -dt plumed.XXXXXX)"
 
-git clone https://github.com/doxygen/doxygen.git
+repo="https://github.com/doxygen/doxygen.git"
 
-cd doxygen
-
-if [ -n "$1" ] ; then
-  echo "installing doxygen $version"
+if [ -n "$1" ]; then
   version=$1
+  echo "installing doxigen $version"
 else
-  echo "installing latest doxygen"
-  version=$(git tag | tail -n 1)
+  # getting the latest version without downloading the repo
+  version=$(
+    git -c 'versionsort.suffix=-' \
+      ls-remote --exit-code --refs --sort='version:refname' --tags "$repo" 'Release_*_*_*' \
+      | tail --lines=1 \
+      | cut --delimiter='/' --fields=3
+  )
+  echo "installing latest doxigen ($version)"
 fi
 
-git checkout $version
+#cloning ONLY the code we need
+git clone "$repo" --branch "$version" --depth 1
+cd doxygen
 
 mkdir build
 cd build
@@ -26,4 +32,3 @@ make -j 4
 make install
 
 cd ../
-

.ci/install.lcov

@@ -5,19 +5,25 @@ set -x
 
 cd "$(mktemp -dt plumed.XXXXXX)"
 
-git clone https://github.com/linux-test-project/lcov.git
+repo=https://github.com/linux-test-project/lcov.git
 
-cd lcov
-
-if [ -n "$1" ] ; then
-  echo "installing lcov $version"
+if [ -n "$1" ]; then
   version=$1
+  echo "installing lcov $version"
 else
-  echo "installing latest lcov"
-  version=$(git tag | tail -n 1)
+  # getting the latest version without downloading the repo
+  version=$(
+    git -c 'versionsort.suffix=-' \
+      ls-remote --exit-code --refs --sort='version:refname' --tags "$repo" 'v*.*.*' \
+      | tail --lines=1 \
+      | cut --delimiter='/' --fields=3
+  )
+  echo "installing latest cppcheck ($version)"
+  echo "installing latest lcov ($version)"
 fi
 
-git checkout $version
+#cloning ONLY the code we need
+git clone "$repo" --branch "$version" --depth 1
+cd lcov
 
 make install PREFIX="$HOME/opt"
-

src/tools/LatticeReduction.cpp

@@ -23,6 +23,7 @@
 #include "Exception.h"
 #include <cstdio>
 #include <cmath>
+#include <iomanip>
 
 namespace PLMD {
 
@@ -34,14 +35,26 @@ void LatticeReduction::sort(Vector v[3]) {
   m[0]=modulo2(v[0]);
   m[1]=modulo2(v[1]);
   m[2]=modulo2(v[2]);
-  for(int i=0; i<3; i++)
-    for(int j=i+1; j<3; j++)
+  for(int i=0; i<3; i++) {
+    for(int j=i+1; j<3; j++) {
       if(m[i]>m[j]) {
         std::swap(v[i],v[j]);
         std::swap(m[i],m[j]);
       }
-  plumed_assert(m[0]<=m[1]*onePlusEpsilon);
-  plumed_assert(m[1]<=m[2]*onePlusEpsilon);
+    }
+  }
+  if(m[0]>m[1]*onePlusEpsilon) {
+    plumed_error() << std::scientific << std::setprecision(17)
+                   << "v[0] " << v[0] << " " << "m[0] " << m[0] <<"\n"
+                   << "v[1] " << v[1] << " " << "m[1] " << m[1] <<"\n"
+                   << "v[2] " << v[2] << " " << "m[2] " << m[2] <<"\n";
+  }
+  if(m[1]>m[2]*onePlusEpsilon) {
+    plumed_error() << std::scientific << std::setprecision(17)
+                   << "v[0] " << v[0] << " " << "m[0] " << m[0] <<"\n"
+                   << "v[1] " << v[1] << " " << "m[1] " << m[1] <<"\n"
+                   << "v[2] " << v[2] << " " << "m[2] " << m[2] <<"\n";
+  }
 }
 
 void LatticeReduction::reduce(Vector&a,Vector&b) {