Merge pull request #1354 from Iximiel/feature/linkedCellsInNL

Using LinkCells in NeigborList

Author: carlocamilloni

.astyle.options.orig

@@ -0,0 +1,13 @@
+# long options can be written without the preceding '--'
+suffix=none #equivalent to "-n"
+style=attach
+add-braces
+indent=spaces=2
+break-one-line-headers
+
+# old options
+#suffix=none
+#indent=spaces=2
+#keep-one-line-statements
+#keep-one-line-blocks
+# end old options

.clang-format

@@ -0,0 +1 @@
+DisableFormat: true

asd

@@ -0,0 +1 @@
+Artistic Style Version 3.1

mycppcheck.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+#formatted with shfmt v3.6.0 https://github.com/mvdan/sh/releases
+function usage() {
+    echo "${0#*/} Runs cppcheck ONLY on the files in src that have changed from the selected base branch"
+    echo 'By default it uses "master" as the base branch, but you can change it with --rev=REV:'
+    echo ""
+    echo "usage: ${0#*/} [--base=REV] change the base branch to use as base for the diff"
+    echo "       ${0#*/} -h|--help   print this help"
+    echo ""
+    echo "for example \`${0#*/} --base=upstream/master\`"
+}
+
+baserev=${PLMD_MYCCPCHECK_REV:-master}
+
+for arg; do
+    case $arg in
+    --base=*) baserev=${arg#*=} ;;
+    -h | --help)
+        usage
+        exit 0
+        ;;
+    *)
+        usage
+        exit 1
+        ;;
+    esac
+done
+srcdir=$(git rev-parse --show-toplevel)
+
+cd "$srcdir" >/dev/null || {
+    echo "Could not cd to $srcdir"
+    exit 1
+}
+
+files=$(
+    git diff-index --diff-filter=ACMR "$baserev" | awk '/src.*(\.h|\.cpp|\.inc\.in)/{print $6}'
+)
+# shellcheck disable=SC2086
+cppcheck --std=c++17 -j 4 --platform=unix64 --language=c++ \
+    -U__GNUG__ -U__PLUMED_HAS_EXTERNAL_LAPACK -U__PLUMED_HAS_EXTERNAL_BLAS \
+    -UGMX_CYGWIN -UF77_NO_UNDERSCORE -U_GLIBCXX_DEBUG -DNDEBUG -U__PLUMED_PBC_WHILE \
+    -U__PLUMED_HAS_ASMJIT \
+    -D__PLUMED_WRAPPER_CXX_EXPLICIT=explicit \
+    --config-exclude=small_vector/ \
+    --template='[{file}:{line}] ({severity}) :{id}: {message}' --enable=all --suppress=missingIncludeSystem --inline-suppr --force \
+    $files

regtest/basic/rt-make-FSUM/main.cpp

@@ -1,23 +1,13 @@
 #include "plumed/tools/Tools.h"
+
+#include "testUtils.h"
+
 #include <iostream>
 #include <fstream>
 #include <iomanip>
 #include <string>
 using namespace PLMD;
 
-class tee {
-//TODO:: put this tee into a common test utilities lib
-  std::ofstream ofs;
-public:
-  tee(std::string filename) : ofs(filename) {}
-  template<typename T>
-  tee& operator<<(const T& t) {
-    ofs<<t;
-    std::cout <<t;
-    return *this;
-  }
-};
-
 template<typename T>
 using FSUM=PLMD::Tools::FastStringUnorderedMap<T>;
 

regtest/basic/rt-make-getwords/main.cpp

@@ -1,23 +1,11 @@
 #include "plumed/tools/Tools.h"
+#include "testUtils.h"
 #include <fstream>
 #include <iomanip>
 #include <iostream>
 
 using namespace PLMD;
 
-class tee {
-//TODO:: put this tee into a common test utilities lib
-  std::ofstream ofs;
-public:
-  tee(std::string filename) : ofs(filename) {}
-  template<typename T>
-  tee& operator<<(const T& t) {
-    ofs<<t;
-    std::cout <<t;
-    return *this;
-  }
-};
-
 int main() {
   try {
 //NOTE:: We are simply checking that gw has the expected behaviour

regtest/basic/rt-make-view/main.cpp

@@ -3,6 +3,8 @@
 #include "plumed/tools/Stopwatch.h"
 #include "plumed/tools/View.h"
 
+#include "testUtils.h"
+
 #include <numeric>
 #include <fstream>
 #include <array>
@@ -14,24 +16,6 @@
 using PLMD::View;
 
 #define displaycall(x) #x << " = " << (x)
-///A very barebone tee implementation
-class tee {
-  std::ofstream ofs;
-public:
-  tee(std::string filename) : ofs(filename) {}
-  template<typename T>
-  tee& operator<<(const T& t) {
-    ofs<<t;
-    std::cout <<t;
-    return *this;
-  }
-  template<typename Iterable>
-  tee&  dump(const Iterable& v) {
-    std::copy(v.begin(),v.end(),std::ostream_iterator<double>(ofs," "));
-    std::copy(v.begin(),v.end(),std::ostream_iterator<double>(std::cout," "));
-    return *this;
-  }
-};
 
 void basics(tee& out);
 void nonspanlikeInteractions(tee& out);

regtest/basic/rt-make-view2D/main.cpp

@@ -3,6 +3,8 @@
 #include "plumed/tools/Stopwatch.h"
 #include "plumed/tools/View2D.h"
 
+#include "testUtils.h"
+
 #include <numeric>
 #include <fstream>
 #include <array>
@@ -16,18 +18,6 @@ using PLMD::View;
 using PLMD::View2D;
 
 #define displaycall(x) #x << " = " << (x)
-///A very barebone tee implementation
-class tee {
-  std::ofstream ofs;
-public:
-  tee(std::string filename) : ofs(filename) {}
-  template<typename T>
-  tee& operator<<(const T& t) {
-    ofs<<t;
-    std::cout <<t;
-    return *this;
-  }
-};
 
 void basics(tee& out);
 void nonspanlikeInteractions(tee& out);

regtest/basic/rt-NeigbourlistInitialization/Makefile renamed to regtest/basic/rt42-cells-cos/Makefile

@@ -0,0 +1,28 @@
+#! FIELDS time s
+ 0.000000   0.0000
+ 1.000000   0.0000
+ 2.000000   0.0000
+ 3.000000   0.0000
+ 4.000000   0.0000
+ 5.000000   0.0000
+ 6.000000   0.0000
+ 7.000000   0.0000
+ 8.000000   0.0000
+ 9.000000   0.0000
+ 10.000000   0.0000
+ 11.000000   0.0000
+ 12.000000   0.0000
+ 13.000000   0.0000
+ 14.000000   0.0000
+ 15.000000   0.0000
+ 16.000000   0.0000
+ 17.000000   0.0000
+ 18.000000   0.0000
+ 19.000000   0.0000
+ 20.000000   0.0000
+ 21.000000   0.0000
+ 22.000000   0.0000
+ 23.000000   0.0000
+ 24.000000   0.0000
+ 25.000000   0.0000
+ 26.000000   0.0000