Major overhaul and enhancement of cluster analysis code.

CMakeLists.txt

@@ -3,9 +3,9 @@ project(cpptraj NONE)
 
 #version number
 #---------------------------------------------------------------------------------------------------------------------------------------------------------------------
-set(cpptraj_MAJOR_VERSION 4)
-set(cpptraj_MINOR_VERSION 3)
-set(cpptraj_TWEAK_VERSION 4)
+set(cpptraj_MAJOR_VERSION 6)
+set(cpptraj_MINOR_VERSION 0)
+set(cpptraj_TWEAK_VERSION 0)
 
 set(cpptraj_VERSION "${cpptraj_MAJOR_VERSION}.${cpptraj_MINOR_VERSION}.${cpptraj_TWEAK_VERSION}")
 
@@ -49,10 +49,12 @@ if(NOT INSIDE_AMBER)
 	set(BUNDLE_SIGNATURE CPTJ)
 	include(Packaging)
 
-	# header installation option
+	# build options
 	option(INSTALL_HEADERS "Copy headers to the include/cpptraj folder of the install directory.  Useful for building with pytraj." FALSE)
 
 	option(BUILD_PARALLEL_COMBINATIONS "If true, then combinations of all enabled parallelizations will be built, e.g. cpptraj.OMP.MPI and cpptraj.OMP.MPI.cuda" FALSE)
+
+	option(INSTALL_TESTS "Copy tests to the test/ folder of the install directory" FALSE)
 else()
 	set(INSTALL_HEADERS FALSE)
 	set(BUILD_PARALLEL_COMBINATIONS FALSE)
@@ -67,4 +69,4 @@ add_subdirectory(test)
 #--------------------------------------------------------------	
 if(NOT INSIDE_AMBER)
 	print_build_report()
-endif()
+endif()

devtools/CheckForMissingSource.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+MAKE_SOURCES=`ls *files`
+if [ -z "$MAKE_SOURCES" ] ; then
+  MAKE_SOURCES=Makefile
+fi
+CMAKE_SOURCES=CMakeLists.txt
+
+echo "Make sources  : $MAKE_SOURCES"
+echo "Cmake sources : $CMAKE_SOURCES"
+
+if [ ! -f "$MAKE_SOURCES" ] ; then
+  echo "Make sources not found."
+  exit 1
+fi
+
+if [ ! -f "$CMAKE_SOURCES" ] ; then
+  echo "Cmake sources not found."
+  exit 1
+fi
+
+SOURCES=`ls *.cpp *.c *.F90 2> /dev/null`
+
+for FILE1 in $MAKE_SOURCES $CMAKE_SOURCES ; do
+  for FILE2 in $SOURCES ; do
+    if [ -z "`grep $FILE2 $FILE1`" ] ; then
+      echo "$FILE2 appears to be missing from $FILE1"
+    fi
+  done
+done

devtools/RunCmake.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# Can be used to test the cmake install.
+# Assumes 'git submodule update --init --recursive' has been run in top dir.
+
+if [ -z "$CPPTRAJHOME" ] ; then
+  echo "CPPTRAJHOME must be set."
+  exit 1
+fi
+HOME=$CPPTRAJHOME
+
+installdir=$HOME/install
+if [ ! -d "$installdir" ] ; then
+  mkdir $installdir
+fi
+
+#export BUILD_FLAGS="-DOPENMP=TRUE"
+#export BUILD_FLAGS="-DMPI=TRUE ${BUILD_FLAGS}"
+#-DNetCDF_LIBRARIES_C=$HOME/lib/libnetcdf.so -DNetCDF_INCLUDES=$HOME/include
+COMPILER=gnu
+cmake .. $BUILD_FLAGS -DCOMPILER=${COMPILER^^} -DINSTALL_HEADERS=FALSE \
+         -DCMAKE_INSTALL_PREFIX=$installdir -DCMAKE_LIBRARY_PATH=$HOME/lib \
+         -DPRINT_PACKAGING_REPORT=TRUE 
+