Includes new LV headers

binder/postBuild

@@ -4,4 +4,4 @@ export  PREFIX=$CONDA_DEFAULT_ENV
 git clone https://github.com/jsalvado/SQuIDS.git $HOME/SQuIDS;
 cd $HOME/SQuIDS; ./configure --prefix=$HOME/software --with-gsl-incdir=$PREFIX/include --with-gsl-libdir=$PREFIX/lib; export LD_LIBRARY_PATH=$PREFIX/lib:$LD_LIBRARY_PATH; make; make test; make install; cd -;
 export LD_LIBRARY_PATH="$HOME/software/lib"
- ./configure --prefix=$HOME/software --with-python-bindings --with-boost=$PREFIX/ --with-gsl=$PREFIX --with-squids=$HOME/software --python-bin=python; make python; make test;  make install;
+ ./configure --prefix=$HOME/software --with-python-bindings --with-boost=$PREFIX/ --with-gsl=$PREFIX --with-squids=$HOME/software --python-bin=python; make; make test;  make install;  cd resources/python/src; make;

binder/start

@@ -1,5 +1,5 @@
 export PKG_CONFIG_PATH="$HOME/software/lib/pkgconfig:$PKG_CONFIG_PATH";
-export PYTHONPATH=$HOME/lib:$HOME/resources/python/bindings:$PYTHONPATH
+export PYTHONPATH=$HOME/resources/python/bindings/:$PYTHONPATH
 export LD_LIBRARY_PATH="$HOME/software/lib":"/srv/conda/envs/notebook"
 echo $PYTHONPATH
 exec "$@"

configure

@@ -1,69 +1,14 @@
 #!/bin/bash
 
-check_os_arch(){
-	if [ -x /usr/bin/lsb_release ]; then
-		OS_DISTRIB=$(lsb_release -si|tr '[:upper:]' '[:lower:]')
-		OS_VERSION=`lsb_release -sr`
-	elif [ -e /etc/os-release ]; then
-		OS_DISTRIB=$(cat /etc/os-release|grep '^ID='|cut -d '=' -f 2|sed s/\"//g|tr '[:upper:]' '[:lower:]')
-		OS_VERSION=$(cat /etc/os-release|grep '^VERSION='|cut -d '=' -f 2|cut -d ' ' -f 1|sed s/\"//g)
-	elif [ -e /etc/redhat-release ]; then
-		OS_DISTRIB="centos"
-		OS_VERSION=$(cat /etc/redhat-release|sed s/\ /\\\\n/g|grep '\.')
-	else
-		OS_DISTRIB=$(uname -s|tr '[:upper:]' '[:lower:]')
-		OS_VERSION=$(uname -r)
-	fi
-	ARCH=$(uname -m)
-	OS_NAME=$(uname -s)
-
-	case $OS_DISTRIB in
-		"redhatenterpriseclient" | "redhatenterpriseserver" | "rhel" | "scientificsl" | "scientific" | "centos" | "scientificfermi" | "scientificcernslc")
-			OS_DISTRIB="RHEL"
-			OS_VERSION=$(echo "${VERSION}" | cut -d '.' -f 1)
-			;;
-		"ubuntu")
-			OS_DISTRIB="Ubuntu"
-			;;
-		"debian")
-			OS_DISTRIB="Ubuntu"
-			;;
-		"linuxmint")
-			OS_DISTRIB="Ubuntu"
-			;;
-		"freebsd")
-			OS_DISTRIB="FreeBSD"
-			OS_VERSION=$(uname -r | cut -d '.' -f 1)
-			ARCH=$(uname -p)
-			;;
-		"darwin")
-			OS_DISTRIB="OSX"
-			OS_VERSION=$(uname -r | cut -d '.' -f 1)
-			;;
-		"linux")
-			if echo $OS_VERSION | grep -q '\.el7\.\?'; then
-				OS_DISTRIB="RHEL"
-				OS_VERSION=7
-			elif echo $OS_VERSION | grep -q '\.el6\.\?'; then
-				OS_DISTRIB="RHEL"
-				OS_VERSION=6
-			elif echo $OS_VERSION | grep -q '\.el5\.\?'; then
-				OS_DISTRIB="RHEL"
-				OS_VERSION=5
-			fi
-	esac
-	OS_ARCH=${OS_DISTRIB}_${OS_VERSION}_${ARCH}
-}
-
 check_pkgconfig(){
 	if [ "$CHECKED_PKGCONFIG" ]; then return; fi
 	echo "Looking for pkg-config..."
-	PKG_CONFIG_BIN=$(which pkg-config 2>&1)
+	PKG_CONFIG_PATH=$(which pkg-config 2>&1)
 	if [ "$?" -ne 0 ]; then
 		echo "Error: pkg-config not found; you will need to specify library locations manually" 1>&2
 		exit 1
 	fi
-	echo " Found $PKG_CONFIG_BIN"
+	echo " Found $PKG_CONFIG_PATH"
 	CHECKED_PKGCONFIG=1
 }
 
@@ -213,7 +158,7 @@ try_find_python(){
 	TMP=`echo "$PYTHON_STDLIBDIR" | sed -n s'|\(.*/lib\)/python'"${PYTHON_VERSION}"'|\1|p'`
 	if [ "$TMP" ]; then POSSIBLE_PYTHON_LIBDIRS="${POSSIBLE_PYTHON_LIBDIRS} ${TMP}"; fi
 	# Ubuntu is special, of course
-	if [ $OS_DISTRIB = "Ubuntu" ]; then
+	if uname -a | grep -i 'ubuntu' > /dev/null; then
 		POSSIBLE_PYTHON_LIBDIRS="${POSSIBLE_PYTHON_LIBDIRS} /usr/lib/$(uname -i)-linux-gnu"
 	fi
 
@@ -272,7 +217,7 @@ try_find_boost(){
 		return
  	fi
 	if [ "$PYTHON_FOUND" ]; then
-		for PYV_SUFFIX in $PYV $PYVM $PYV-mt $PVM-mt ''; do
+		for PYV_SUFFIX in $PYV $PYVM ''; do
 			for BOOST_LIBDIR in $POSSIBLE_BOOST_LIBDIRS; do
 				if [ -d $BOOST_LIBDIR -a \( -e $BOOST_LIBDIR/libboost_python${PYV_SUFFIX}.a -o -e $BOOST_LIBDIR/libboost_python${PYV_SUFFIX}.so -o -e $BOOST_LIBDIR/libboost_python${PYV_SUFFIX}.dylib \) ]; then
 					if [ ! "$PYV_SUFFIX" ]; then
@@ -354,7 +299,7 @@ VERSION=`echo $VERSION_NUM | awk '{
 	print major"."minor"."patch;
 }'`
 
-check_os_arch
+OS_NAME=`uname -s`
 
 GUESS_CC=gcc
 GUESS_CXX=g++
@@ -735,8 +680,7 @@ echo "SQUIDS_LDFLAGS=$SQUIDS_LDFLAGS" >> ./Makefile
 if [ "$PYTHON_BINDINGS" ]; then
 	echo "PYTHON_CFLAGS=$PYTHON_CFLAGS" >> ./Makefile
 	echo "PYTHON_LDFLAGS=$PYTHON_LDFLAGS" >> ./Makefile
-	echo "BOOST_CFLAGS=$BOOST_CFLAGS" >> ./Makefile
-	echo "BOOST_PYTHON_LDFLAGS=$BOOST_LDFLAGS $BOOST_PYTHON_LDFLAGS" >> ./Makefile
+	echo "BOOST_PYTHON_LDFLAGS=$BOOST_PYTHON_LDFLAGS" >> ./Makefile
 	echo "PYTHON_MODULEDIR=$PYTHON_MODULEDIR" >> ./Makefile
 	echo "NUMPY_CFLAGS=$NUMPY_CFLAGS" >> ./Makefile
 fi
@@ -854,8 +798,8 @@ install: $(DYN_PRODUCT) $(STAT_PRODUCT)
 	@cp "$(INCnuSQUIDS)"/nuSQuIDS/*.h "$(PREFIX)/include/nuSQuIDS"
 	@echo Installing libraries in $(PREFIX)/$(INSTALL_LIBDIR)
 	@mkdir -p "$(PREFIX)/$(INSTALL_LIBDIR)"
-	@LC_ALL=C sed "'${REPLACE_INSTALL_FLAG}'" < $(DYN_PRODUCT) > "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME)$(DYN_SUFFIX)"
-	@LC_ALL=C sed "'${REPLACE_INSTALL_FLAG}'" < $(STAT_PRODUCT) > "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME).a"
+	@LANG=C sed "'${REPLACE_INSTALL_FLAG}'" < $(DYN_PRODUCT) > "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME)$(DYN_SUFFIX)"
+	@LANG=C sed "'${REPLACE_INSTALL_FLAG}'" < $(STAT_PRODUCT) > "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME).a"
 	@chmod 755 "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME)$(DYN_SUFFIX)" "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME).a" 
 	@echo Installing config information in $(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig
 	@mkdir -p "$(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig"
@@ -875,8 +819,8 @@ uninstall:
 	@echo Removing headers from $(PREFIX)/include/nuSQuIDS
 	@rm -rf "$(PREFIX)/include/nuSQuIDS"
 	@echo Removing libraries from $(PREFIX)/$(INSTALL_LIBDIR)
-	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME)$(DYN_SUFFIX)"
-	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/lib$(NAME).a"
+	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/$(DYN_PRODUCT)"
+	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/$(STAT_PRODUCT)"
 	@echo Removing config information from $(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig
 	@rm -f "$(PREFIX)/$(INSTALL_LIBDIR)/pkgconfig/nusquids.pc"
 ' >> ./Makefile
@@ -892,7 +836,7 @@ $(PYTHON_LIB) : build/nuSQUIDSpy.o $(STAT_PRODUCT)
 
 build/nuSQUIDSpy.o : resources/python/src/nuSQUIDSpy.cpp
 	@echo Compiling python bindings
-	@$(CXX) $(CXXFLAGS) -c -Iresources/python/inc $(PYTHON_CFLAGS) $(BOOST_CFLAGS) $(NUMPY_CFLAGS) $(CFLAGS) $< -o $@
+	@$(CXX) $(CXXFLAGS) -c -Iresources/python/inc $(PYTHON_CFLAGS) $(NUMPY_CFLAGS) $(CFLAGS) $< -o $@
 
 python-install : $(PYTHON_LIB)
 	@echo Installing python module in $(PYTHON_MODULEDIR)
@@ -908,9 +852,9 @@ fi
 
 echo "
 export CXX=\"${CXX}\"
-export CFLAGS=\"${CFLAGS} -I${SOURCE_PATH}/inlude ${SQUIDS_CFLAGS} ${GSL_CFLAGS} ${HDF5_CFLAGS}\"
+export CFLAGS=\"${CFLAGS} ${SQUIDS_CFLAGS} ${GSL_CFLAGS} ${HDF5_CFLAGS}\"
 export CXXFLAGS=\"${CXXFLAGS} -std=c++11\"
-export LDFLAGS=\"${LDFLAGS} -L${SOURCE_PATH}/lib -Wl,-rpath -Wl,${SOURCE_PATH}/lib -lnuSQuIDS -lpthread ${SQUIDS_LDFLAGS} ${GSL_LDFLAGS} ${HDF5_LDFLAGS}\"
+export LDFLAGS=\"${LDFLAGS}  -lnuSQuIDS -lpthread ${SQUIDS_LDFLAGS} ${GSL_LDFLAGS} ${HDF5_LDFLAGS}\"
 " > test/env_vars.sh
 if uname | grep -q 'Darwin' ; then
 	printf "export DYLD_LIBRARY_PATH=\"" >> test/env_vars.sh

examples/Bodies/main.cpp

@@ -164,7 +164,7 @@ int main()
   std::cout << "******** Earth Atmospheric Neutrino Osc **********" << std::endl;
 
   std::shared_ptr<EarthAtm> earth_atm = std::make_shared<EarthAtm>();
-  auto earth_atm_track = std::make_shared<EarthAtm::Track>(earth_atm->MakeTrack(phi));
+  std::shared_ptr<EarthAtm::Track> earth_atm_track = std::make_shared<EarthAtm::Track>(phi);
 
   nus.Set_Body(earth_atm);
   nus.Set_Track(earth_atm_track);
@@ -216,7 +216,7 @@ int main()
   std::cout << "***** Earth Modified Atmospheric Neutrino Osc ****" << std::endl;
 
   std::shared_ptr<EarthMod> earth_mod = std::make_shared<EarthMod>(0.1,0.1,0.1);
-  auto earth_mod_track = std::make_shared<EarthMod::Track>(earth_atm->MakeTrack(phi));
+  std::shared_ptr<EarthMod::Track> earth_mod_track = std::make_shared<EarthMod::Track>(phi);
   earth_mod->Mod(0.1,0.1,0.1);
 
   nus.Set_Body(earth_mod);

examples/HDF5_Write_Read/plot.plt

@@ -1,4 +1,4 @@
-#!/usr/bin/env gnuplot
+#!/usr/bin/env gnuplot -persist
 if ( GPVAL_VERSION >= 4.4 && strstrt(GPVAL_TERMINALS, 'wxt') > 0 ) set terminal wxt persist
 if ( GPVAL_VERSION >= 4.4 && strstrt(GPVAL_TERMINALS, 'qt') > 0 ) set terminal qt persist
 if ( GPVAL_VERSION >= 4.4 && strstrt(GPVAL_TERMINALS, 'wxt') == 0 && strstrt(GPVAL_TERMINALS, 'qt') == 0 ) print "wxt and qt terminals not available, proceeding with default"

examples/HDF5_Write_Read/read.cpp

@@ -38,10 +38,12 @@ int main()
   squids::Const units;
 
   //Here we create the nusquids object reading the state from the hdf5 file.
-  nuSQUIDS inus("./initial_state.hdf5");
-  nuSQUIDS fnus("./final_state.hdf5");
+  //nuSQUIDS inus("./initial_state.hdf5");
+  //nuSQUIDS fnus("./final_state.hdf5");
 
-
+  nuSQUIDSAtm<> inus("./pion_atmospheric_initial.hdf5");
+  nuSQUIDSAtm<> fnus("./pion_atmospheric_2441_1.000000_0.000000_0.160875_0.000000_0.000000_0.000000.hdf5");
+
   //In this part we will save the values in a txt file to be able to plot or manipulate later.
   //Notice that this is not going to have all the information about the quantum evolution, for that 
   //we need to save the information using the HDF5 writing function.
@@ -60,7 +62,7 @@ int main()
     file << lE << " " << E << " ";
     for(int fl=0; fl<numneu; fl++){
       //the ration in the second column is with the initial muon flux, the others are zero.
-      file << " " <<  fnus.EvalFlavor(fl, E, 0) << " " <<  fnus.EvalFlavor(fl, E, 0)/inus.EvalFlavor(1, E, 0);
+      file << " " <<  fnus.EvalFlavor(fl, -1,E) << " " <<  fnus.EvalFlavor(fl,-1, E)/inus.EvalFlavor(1, -1,E);
     }
     file << std::endl;
   }