diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
index b357e340e..9615297ca 100644
--- a/src/GPU/Install.sh
+++ b/src/GPU/Install.sh
@@ -1,186 +1,186 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude GPU info
 # do not install child files if parent does not exist
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*gpu[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/gpu |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lgpu |' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(gpu_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(gpu_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(gpu_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/gpu\/Makefile.lammps\
+include ..\/..\/lib\/gpu\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   if (test -e ../pair_yukawa.cpp) then
     cp pair_yukawa_gpu.cpp ..
     cp pair_yukawa_gpu.h ..
   fi
   
   if (test -e ../pair_table.cpp) then
     cp pair_table_gpu.cpp ..
     cp pair_table_gpu.h ..
   fi
 
   if (test -e ../pair_buck.cpp) then
     cp pair_buck_gpu.cpp ..
     cp pair_buck_gpu.h ..
   fi
 
   if (test -e ../pair_buck_coul_cut.cpp) then
     cp pair_buck_coul_cut_gpu.cpp ..
     cp pair_buck_coul_cut_gpu.h ..
   fi
 
   if (test -e ../pair_buck_coul_long.cpp) then
     cp pair_buck_coul_long_gpu.cpp ..
     cp pair_buck_coul_long_gpu.h ..
   fi
   
   if (test -e ../pair_eam.cpp) then
     cp pair_eam_gpu.cpp ..
     cp pair_eam_gpu.h ..
     cp pair_eam_alloy_gpu.cpp ..
     cp pair_eam_alloy_gpu.h ..
     cp pair_eam_fs_gpu.cpp ..
     cp pair_eam_fs_gpu.h ..
   fi
   
   if (test -e ../pair_gayberne.cpp) then
     cp pair_gayberne_gpu.cpp ..
     cp pair_gayberne_gpu.h ..
     cp pair_resquared_gpu.cpp ..
     cp pair_resquared_gpu.h ..
   fi
   
   if (test -e ../pair_lj_cut_coul_long.cpp) then
     cp pair_lj_cut_coul_long_gpu.cpp ..
     cp pair_lj_cut_coul_long_gpu.h ..
   fi
 
   if (test -e ../pair_lj_class2.cpp) then
     cp pair_lj_class2_gpu.cpp ..
     cp pair_lj_class2_gpu.h ..
   fi
 
   if (test -e ../pair_lj_class2_coul_long.cpp) then
     cp pair_lj_class2_coul_long_gpu.cpp ..
     cp pair_lj_class2_coul_long_gpu.h ..
   fi
 
   if (test -e ../pair_lj_charmm_coul_long.cpp) then
     cp pair_lj_charmm_coul_long_gpu.cpp ..
     cp pair_lj_charmm_coul_long_gpu.h ..
   fi
 
   if (test -e ../pair_coul_long.cpp) then
     cp pair_coul_long_gpu.cpp ..
     cp pair_coul_long_gpu.h ..
   fi
 
   if (test -e ../pair_lj_sdk.cpp) then
     cp pair_lj_sdk_gpu.cpp ..
     cp pair_lj_sdk_gpu.h ..
   fi
 
   if (test -e ../pair_lj_sdk_coul_long.cpp) then
     cp pair_lj_sdk_coul_long_gpu.cpp ..
     cp pair_lj_sdk_coul_long_gpu.h ..
   fi
 
   if (test -e ../pppm.cpp) then
     cp pppm_gpu.cpp ..
     cp pppm_gpu.h ..
   fi
 
   cp pair_lj_cut_gpu.cpp ..
   cp pair_morse_gpu.cpp ..
   cp pair_lj96_cut_gpu.cpp ..
   cp pair_lj_expand_gpu.cpp ..
   cp pair_lj_cut_coul_cut_gpu.cpp ..
 
   cp fix_gpu.cpp ..
 
   cp pair_lj_cut_gpu.h ..
   cp pair_morse_gpu.h ..
   cp pair_lj96_cut_gpu.h ..
   cp pair_lj_expand_gpu.h ..
   cp pair_lj_cut_coul_cut_gpu.h ..
   
   cp fix_gpu.h ..
   cp gpu_extra.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*gpu[^ \t]* //' ../Makefile.package
   fi
   
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../pair_buck_coul_cut_gpu.cpp
   rm -f ../pair_buck_coul_long_gpu.cpp
   rm -f ../pair_buck_gpu.cpp
   rm -f ../pair_coul_long_gpu.cpp
   rm -f ../pair_eam_alloy_gpu.cpp
   rm -f ../pair_eam_fs_gpu.cpp
   rm -f ../pair_eam_gpu.cpp
   rm -f ../pair_gayberne_gpu.cpp
   rm -f ../pair_lj96_cut_gpu.cpp
   rm -f ../pair_lj_charmm_coul_long_gpu.cpp
   rm -f ../pair_lj_class2_coul_long_gpu.cpp
   rm -f ../pair_lj_class2_gpu.cpp
   rm -f ../pair_lj_cut_coul_cut_gpu.cpp
   rm -f ../pair_lj_cut_coul_long_gpu.cpp
   rm -f ../pair_lj_cut_gpu.cpp
   rm -f ../pair_lj_expand_gpu.cpp
   rm -f ../pair_lj_sdk_coul_long_gpu.cpp
   rm -f ../pair_lj_sdk_gpu.cpp
   rm -f ../pair_morse_gpu.cpp
   rm -f ../pair_resquared_gpu.cpp
   rm -f ../pair_table_gpu.cpp
   rm -f ../pair_yukawa_gpu.cpp
   rm -f ../pppm_gpu.cpp
 
   rm -f ../fix_gpu.cpp
 
   rm -f ../pair_buck_coul_cut_gpu.h
   rm -f ../pair_buck_coul_long_gpu.h
   rm -f ../pair_buck_gpu.h
   rm -f ../pair_coul_long_gpu.h
   rm -f ../pair_eam_alloy_gpu.h
   rm -f ../pair_eam_fs_gpu.h
   rm -f ../pair_eam_gpu.h
   rm -f ../pair_gayberne_gpu.h
   rm -f ../pair_lj96_cut_gpu.h
   rm -f ../pair_lj_charmm_coul_long_gpu.h
   rm -f ../pair_lj_class2_coul_long_gpu.h
   rm -f ../pair_lj_class2_gpu.h
   rm -f ../pair_lj_cut_coul_cut_gpu.h
   rm -f ../pair_lj_cut_coul_long_gpu.h
   rm -f ../pair_lj_cut_gpu.h
   rm -f ../pair_lj_expand_gpu.h
   rm -f ../pair_lj_sdk_coul_long_gpu.h
   rm -f ../pair_lj_sdk_gpu.h
   rm -f ../pair_morse_gpu.h
   rm -f ../pair_resquared_gpu.h
   rm -f ../pair_table_gpu.h
   rm -f ../pair_yukawa_gpu.h
   rm -f ../pppm_gpu.h
 
   rm -f ../fix_gpu.h
   rm -f ../gpu_extra.h
   
 fi
 
diff --git a/src/KIM/Install.sh b/src/KIM/Install.sh
index 8e089f1dd..c485cf969 100644
--- a/src/KIM/Install.sh
+++ b/src/KIM/Install.sh
@@ -1,37 +1,37 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude package info
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kim_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kim_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kim_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*KIM.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
-    sed -i '4 i \
-include ..\/KIM\/Makefile.lammps\
+    sed -i -e '4 i \
+include ..\/KIM\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp pair_kim.cpp ..
   cp pair_kim.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*KIM.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../pair_kim.cpp
   rm -f ../pair_kim.h
 
 fi
diff --git a/src/MEAM/Install.sh b/src/MEAM/Install.sh
index 6481348e6..09b1b89d1 100644
--- a/src/MEAM/Install.sh
+++ b/src/MEAM/Install.sh
@@ -1,42 +1,42 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude package info
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*meam[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/meam |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/meam |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lmeam |' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(meam_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(meam_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(meam_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*meam.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/meam\/Makefile.lammps\
+include ..\/..\/lib\/meam\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp pair_meam.cpp ..
 
   cp pair_meam.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*meam[^ \t]* //' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*meam.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../pair_meam.cpp
 
   rm -f ../pair_meam.h
 
 fi
diff --git a/src/POEMS/Install.sh b/src/POEMS/Install.sh
index a7f228fca..e5f5d2bd6 100644
--- a/src/POEMS/Install.sh
+++ b/src/POEMS/Install.sh
@@ -1,39 +1,39 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude POEMS info
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*poems[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/poems |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/poems |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lpoems |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/poems\/Makefile.lammps\
+include ..\/..\/lib\/poems\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp fix_poems.cpp ..
 
   cp fix_poems.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*poems[^ \t]* //' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../fix_poems.cpp
 
   rm -f ../fix_poems.h
 
 fi
diff --git a/src/REAX/Install.sh b/src/REAX/Install.sh
index d1a4587d7..0cb94a6b7 100644
--- a/src/REAX/Install.sh
+++ b/src/REAX/Install.sh
@@ -1,48 +1,48 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude REAX info
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*reax[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/reax |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/reax |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lreax |' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(reax_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(reax_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(reax_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*reax.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/reax\/Makefile.lammps\
+include ..\/..\/lib\/reax\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp pair_reax.cpp ..
   cp pair_reax.h ..
   cp pair_reax_fortran.h ..
 
   cp fix_reax_bonds.h ..
   cp fix_reax_bonds.cpp ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*reax[^ \t]* //' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*reax.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../pair_reax.cpp
   rm -f ../pair_reax.h
   rm -f ../pair_reax_fortran.h
 
   rm -f ../fix_reax_bonds.h
   rm -f ../fix_reax_bonds.cpp
 
 fi
diff --git a/src/USER-ATC/Install.sh b/src/USER-ATC/Install.sh
index aea2e9607..1dc236491 100755
--- a/src/USER-ATC/Install.sh
+++ b/src/USER-ATC/Install.sh
@@ -1,40 +1,40 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude ATC info
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*atc[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/atc |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/atc |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-latc |' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-atc_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-atc_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/atc\/Makefile.lammps\
+include ..\/..\/lib\/atc\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp fix_atc.h ..
   cp fix_atc.cpp ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*atc[^ \t]* //' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../fix_atc.h
   rm -f ../fix_atc.cpp
 
 fi
diff --git a/src/USER-AWPMD/Install.sh b/src/USER-AWPMD/Install.sh
index ceed71fce..47db11411 100644
--- a/src/USER-AWPMD/Install.sh
+++ b/src/USER-AWPMD/Install.sh
@@ -1,49 +1,49 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude AWPMD info
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*awpmd[^ \t]* //g' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/awpmd/ivutils/include -I../../lib/awpmd/systems/interact |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/awpmd |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lawpmd |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-awpmd_SYSPATH) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-awpmd_SYSLIB) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/awpmd\/Makefile.lammps\
+include ..\/..\/lib\/awpmd\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp atom_vec_wavepacket.cpp ..
   cp fix_nve_awpmd.cpp ..
   cp pair_awpmd_cut.cpp ..
 
   cp atom_vec_wavepacket.h ..
   cp fix_nve_awpmd.h ..
   cp pair_awpmd_cut.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*awpmd[^ \t]* //g' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../atom_vec_wavepacket.cpp
   rm -f ../fix_nve_awpmd.cpp
   rm -f ../pair_awpmd_cut.cpp
 
   rm -f ../atom_vec_wavepacket.h
   rm -f ../fix_nve_awpmd.h
   rm -f ../pair_awpmd_cut.h
 
 fi
diff --git a/src/USER-COLVARS/Install.sh b/src/USER-COLVARS/Install.sh
index fa4ea390d..ad21cd182 100755
--- a/src/USER-COLVARS/Install.sh
+++ b/src/USER-COLVARS/Install.sh
@@ -1,45 +1,45 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude CUDA info
 # do not install child files if parent does not exist
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*colvars[^ \t]* //g' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/colvars |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/colvars |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lcolvars |' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(colvars_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(colvars_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(colvars_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/colvars\/Makefile.lammps\
+include ..\/..\/lib\/colvars\/Makefile.lammps
 ' ../Makefile.package.settings
 
   fi
 
   cp colvarproxy_lammps.h ..
   cp colvarproxy_lammps.cpp ..
   cp fix_colvars.h ..
   cp fix_colvars.cpp ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*colvars[^ \t]* //g' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../colvarproxy_lammps.h
   rm -f ../colvarproxy_lammps.cpp
   rm -f ../fix_colvars.h
   rm -f ../fix_colvars.cpp
 fi
diff --git a/src/USER-CUDA/Install.sh b/src/USER-CUDA/Install.sh
index 739a9914c..af1d3a7f0 100755
--- a/src/USER-CUDA/Install.sh
+++ b/src/USER-CUDA/Install.sh
@@ -1,362 +1,362 @@
 # Install/unInstall package files in LAMMPS
 # edit 2 Makefile.package files to include/exclude CUDA info
 # do not install child files if parent does not exist
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*cuda[^ \t]* //g' ../Makefile.package
     sed -i -e 's/[^ \t]*CUDA[^ \t]* //g' ../Makefile.package
     sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/cuda -DLMP_USER_CUDA |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/cuda |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-llammpscuda |' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-cuda_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-cuda_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-cuda_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*cuda.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
-include ..\/..\/lib\/cuda\/Makefile.lammps\
+include ..\/..\/lib\/cuda\/Makefile.lammps
 ' ../Makefile.package.settings
 
   fi
 
   # force rebuild of files with LMP_USER_CUDA switch
 
   touch ../accelerator_cuda.h
 
   if (test -e ../atom_vec_angle.cpp) then
     cp atom_vec_angle_cuda.cpp ..
     cp atom_vec_angle_cuda.h ..
   fi
 
   if (test -e ../atom_vec_full.cpp) then
     cp atom_vec_full_cuda.cpp ..
     cp atom_vec_full_cuda.h ..
   fi
 
   if (test -e ../fix_freeze.cpp) then
     cp fix_freeze_cuda.cpp ..
     cp fix_freeze_cuda.h ..
   fi
 
   if (test -e ../pair_born_coul_long.cpp) then
     cp pair_born_coul_long_cuda.cpp ..
     cp pair_born_coul_long_cuda.h ..
   fi
 
   if (test -e ../pair_buck_coul_long.cpp) then
     cp pair_buck_coul_long_cuda.cpp ..
     cp pair_buck_coul_long_cuda.h ..
   fi
 
   if (test -e ../pair_lj_sdk.cpp) then
     cp pair_lj_sdk_cuda.cpp ..
 #    cp pair_lj_sdk_coul_cut_cuda.cpp ..
 #    cp pair_lj_sdk_coul_debye_cuda.cpp ..
     cp pair_lj_sdk_cuda.h ..
 #    cp pair_lj_sdk_coul_cut_cuda.h ..
 #    cp pair_lj_sdk_coul_debye_cuda.h ..
   fi
 
   if (test -e ../pair_lj_sdk_coul_long.cpp) then
     cp pair_lj_sdk_coul_long_cuda.cpp ..
     cp pair_lj_sdk_coul_long_cuda.h ..
   fi
 
   if (test -e ../pppm.cpp) then
     cp pppm_cuda.cpp ..
     cp fft3d_cuda.cpp ..
     cp fft3d_wrap_cuda.cpp ..
     cp pppm_cuda.h ..
     cp fft3d_cuda.h ..
     cp fft3d_wrap_cuda.h ..
     cp pair_lj_cut_coul_long_cuda.cpp ..
     cp pair_lj_cut_coul_long_cuda.h ..
   fi
   
 
   if (test -e ../pair_eam.cpp) then
     cp pair_eam_alloy_cuda.cpp ..
     cp pair_eam_cuda.cpp ..
     cp pair_eam_fs_cuda.cpp ..
     cp pair_eam_alloy_cuda.h ..
     cp pair_eam_cuda.h ..
     cp pair_eam_fs_cuda.h ..
     cp pair_sw_cuda.h ..
     cp pair_sw_cuda.cpp ..
     cp pair_tersoff_cuda.h ..
     cp pair_tersoff_cuda.cpp ..
     cp pair_tersoff_zbl_cuda.h ..
     cp pair_tersoff_zbl_cuda.cpp ..
   fi
 
   if (test -e ../pair_gran_hooke.cpp) then
     cp pair_gran_hooke_cuda.cpp ..
     cp pair_gran_hooke_cuda.h ..
   fi
 
   if (test -e ../pair_lj_charmm_coul_charmm.cpp) then
     cp pair_lj_charmm_coul_charmm_cuda.cpp ..
     cp pair_lj_charmm_coul_charmm_implicit_cuda.cpp ..
     cp pair_lj_charmm_coul_charmm_cuda.h ..
     cp pair_lj_charmm_coul_charmm_implicit_cuda.h ..
     if (test -e ../pair_lj_charmm_coul_long.cpp) then  
       cp pair_lj_charmm_coul_long_cuda.cpp ..
       cp pair_lj_charmm_coul_long_cuda.h ..
     fi
   fi
 
   if (test -e ../pair_lj_class2.cpp) then
     cp pair_lj_class2_coul_cut_cuda.cpp ..
     cp pair_lj_class2_cuda.cpp ..
     cp pair_lj_class2_coul_cut_cuda.h ..
     cp pair_lj_class2_cuda.h ..
     if (test -e ../pair_lj_class2_coul_long.cpp) then
       cp pair_lj_class2_coul_long_cuda.cpp ..
       cp pair_lj_class2_coul_long_cuda.h ..
     fi
   fi 
 
   cp atom_vec_atomic_cuda.cpp ..
   cp atom_vec_charge_cuda.cpp ..
   cp comm_cuda.cpp ..
   cp compute_pe_cuda.cpp ..
   cp compute_pressure_cuda.cpp ..
   cp compute_temp_cuda.cpp ..
   cp compute_temp_partial_cuda.cpp ..
   cp domain_cuda.cpp ..
   cp fix_addforce_cuda.cpp ..
   cp fix_aveforce_cuda.cpp ..
   cp fix_enforce2d_cuda.cpp ..
   cp fix_gravity_cuda.cpp ..
   cp fix_nh_cuda.cpp ..
   cp fix_npt_cuda.cpp ..
   cp fix_nve_cuda.cpp ..
   cp fix_nvt_cuda.cpp ..
   cp fix_set_force_cuda.cpp ..
   cp fix_shake_cuda.cpp ..
   cp fix_temp_berendsen_cuda.cpp ..
   cp fix_temp_rescale_cuda.cpp ..
   cp fix_temp_rescale_limit_cuda.cpp ..
   cp fix_viscous_cuda.cpp ..
   cp modify_cuda.cpp ..
   cp neighbor_cuda.cpp ..
   cp neigh_full_cuda.cpp ..
   cp pair_buck_coul_cut_cuda.cpp ..
   cp pair_buck_cuda.cpp ..
   cp pair_lj96_cut_cuda.cpp ..
   cp pair_lj_cut_coul_cut_cuda.cpp ..
   cp pair_lj_cut_coul_debye_cuda.cpp ..
   cp pair_lj_cut_cuda.cpp ..
   cp pair_lj_cut_experimental_cuda.cpp ..
   cp pair_lj_expand_cuda.cpp ..
   cp pair_lj_gromacs_coul_gromacs_cuda.cpp ..
   cp pair_lj_gromacs_cuda.cpp ..
   cp pair_lj_smooth_cuda.cpp ..
   cp pair_morse_cuda.cpp ..
   cp verlet_cuda.cpp ..
 
   cp cuda.cpp ..
   cp cuda_neigh_list.cpp ..
 
   cp atom_vec_atomic_cuda.h ..
   cp atom_vec_charge_cuda.h ..
   cp comm_cuda.h ..
   cp compute_pe_cuda.h ..
   cp compute_pressure_cuda.h ..
   cp compute_temp_cuda.h ..
   cp compute_temp_partial_cuda.h ..
   cp domain_cuda.h ..
   cp fix_addforce_cuda.h ..
   cp fix_aveforce_cuda.h ..
   cp fix_enforce2d_cuda.h ..
   cp fix_gravity_cuda.h ..
   cp fix_nh_cuda.h ..
   cp fix_npt_cuda.h ..
   cp fix_nve_cuda.h ..
   cp fix_nvt_cuda.h ..
   cp fix_set_force_cuda.h ..
   cp fix_shake_cuda.h ..
   cp fix_temp_berendsen_cuda.h ..
   cp fix_temp_rescale_cuda.h ..
   cp fix_temp_rescale_limit_cuda.h ..
   cp fix_viscous_cuda.h ..
   cp modify_cuda.h ..
   cp neighbor_cuda.h ..
   cp pair_buck_coul_cut_cuda.h ..
   cp pair_buck_cuda.h ..
 
   cp pair_lj96_cut_cuda.h ..
   cp pair_lj_cut_coul_cut_cuda.h ..
   cp pair_lj_cut_coul_debye_cuda.h ..
   cp pair_lj_cut_cuda.h ..
   cp pair_lj_cut_experimental_cuda.h ..
   cp pair_lj_expand_cuda.h ..
   cp pair_lj_gromacs_coul_gromacs_cuda.h ..
   cp pair_lj_gromacs_cuda.h ..
   cp pair_lj_smooth_cuda.h ..
   cp pair_morse_cuda.h ..
   cp verlet_cuda.h ..
 
   cp cuda.h ..
   cp cuda_data.h ..
   cp cuda_modify_flags.h ..
   cp cuda_neigh_list.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*cuda[^ \t]* //g' ../Makefile.package
     sed -i -e 's/[^ \t]*CUDA[^ \t]* //g' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*cuda.*$/d' ../Makefile.package.settings
   fi
 
   # force rebuild of files with LMP_USER_CUDA switch
 
   touch ../accelerator_cuda.h
 
   rm -f ../atom_vec_angle_cuda.cpp
   rm -f ../atom_vec_atomic_cuda.cpp
   rm -f ../atom_vec_charge_cuda.cpp
   rm -f ../atom_vec_full_cuda.cpp
   rm -f ../comm_cuda.cpp
   rm -f ../compute_pe_cuda.cpp
   rm -f ../compute_pressure_cuda.cpp
   rm -f ../compute_temp_cuda.cpp
   rm -f ../compute_temp_partial_cuda.cpp
   rm -f ../domain_cuda.cpp
   rm -f ../fft3d_cuda.cpp
   rm -f ../fft3d_wrap_cuda.cpp
   rm -f ../fix_addforce_cuda.cpp
   rm -f ../fix_aveforce_cuda.cpp
   rm -f ../fix_enforce2d_cuda.cpp
   rm -f ../fix_freeze_cuda.cpp
   rm -f ../fix_gravity_cuda.cpp
   rm -f ../fix_nh_cuda.cpp
   rm -f ../fix_npt_cuda.cpp
   rm -f ../fix_nve_cuda.cpp
   rm -f ../fix_nvt_cuda.cpp
   rm -f ../fix_set_force_cuda.cpp
   rm -f ../fix_shake_cuda.cpp
   rm -f ../fix_temp_berendsen_cuda.cpp
   rm -f ../fix_temp_rescale_cuda.cpp
   rm -f ../fix_temp_rescale_limit_cuda.cpp
   rm -f ../fix_viscous_cuda.cpp
   rm -f ../modify_cuda.cpp
   rm -f ../neighbor_cuda.cpp
   rm -f ../neigh_full_cuda.cpp
   rm -f ../pair_born_coul_long_cuda.cpp
   rm -f ../pair_buck_coul_cut_cuda.cpp
   rm -f ../pair_buck_coul_long_cuda.cpp
   rm -f ../pair_buck_cuda.cpp
   rm -f ../pair_lj_sdk_coul_cut_cuda.cpp
   rm -f ../pair_lj_sdk_coul_debye_cuda.cpp
   rm -f ../pair_lj_sdk_coul_long_cuda.cpp
   rm -f ../pair_lj_sdk_cuda.cpp
   rm -f ../pair_eam_alloy_cuda.cpp
   rm -f ../pair_eam_cuda.cpp
   rm -f ../pair_eam_fs_cuda.cpp
   rm -f ../pair_gran_hooke_cuda.cpp
   rm -f ../pair_lj96_cut_cuda.cpp
   rm -f ../pair_lj_charmm_coul_charmm_cuda.cpp
   rm -f ../pair_lj_charmm_coul_charmm_implicit_cuda.cpp
   rm -f ../pair_lj_charmm_coul_long_cuda.cpp
   rm -f ../pair_lj_class2_coul_cut_cuda.cpp
   rm -f ../pair_lj_class2_coul_long_cuda.cpp
   rm -f ../pair_lj_class2_cuda.cpp
   rm -f ../pair_lj_cut_coul_cut_cuda.cpp
   rm -f ../pair_lj_cut_coul_debye_cuda.cpp
   rm -f ../pair_lj_cut_coul_long_cuda.cpp
   rm -f ../pair_lj_cut_cuda.cpp
   rm -f ../pair_lj_cut_experimental_cuda.cpp
   rm -f ../pair_lj_expand_cuda.cpp
   rm -f ../pair_lj_gromacs_coul_gromacs_cuda.cpp
   rm -f ../pair_lj_gromacs_cuda.cpp
   rm -f ../pair_lj_smooth_cuda.cpp
   rm -f ../pair_morse_cuda.cpp
   rm -f ../pppm_cuda.cpp
   rm -f ../verlet_cuda.cpp
 
   rm -f ../cuda.cpp
   rm -f ../cuda_neigh_list.cpp
 
   rm -f ../atom_vec_angle_cuda.h
   rm -f ../atom_vec_atomic_cuda.h
   rm -f ../atom_vec_charge_cuda.h
   rm -f ../atom_vec_full_cuda.h
   rm -f ../comm_cuda.h
   rm -f ../compute_pe_cuda.h
   rm -f ../compute_pressure_cuda.h
   rm -f ../compute_temp_cuda.h
   rm -f ../compute_temp_partial_cuda.h
   rm -f ../domain_cuda.h
   rm -f ../fft3d_cuda.h
   rm -f ../fft3d_wrap_cuda.h
   rm -f ../fix_addforce_cuda.h
   rm -f ../fix_aveforce_cuda.h
   rm -f ../fix_enforce2d_cuda.h
   rm -f ../fix_freeze_cuda.h
   rm -f ../fix_gravity_cuda.h
   rm -f ../fix_nh_cuda.h
   rm -f ../fix_npt_cuda.h
   rm -f ../fix_nve_cuda.h
   rm -f ../fix_nvt_cuda.h
   rm -f ../fix_set_force_cuda.h
   rm -f ../fix_shake_cuda.h
   rm -f ../fix_temp_berendsen_cuda.h
   rm -f ../fix_temp_rescale_cuda.h
   rm -f ../fix_temp_rescale_limit_cuda.h
   rm -f ../fix_viscous_cuda.h
   rm -f ../modify_cuda.h
   rm -f ../neighbor_cuda.h
   rm -f ../pair_born_coul_long_cuda.h
   rm -f ../pair_buck_coul_cut_cuda.h
   rm -f ../pair_buck_coul_long_cuda.h
   rm -f ../pair_buck_cuda.h
   rm -f ../pair_lj_sdk_coul_cut_cuda.h
   rm -f ../pair_lj_sdk_coul_debye_cuda.h
   rm -f ../pair_lj_sdk_coul_long_cuda.h
   rm -f ../pair_lj_sdk_cuda.h
   rm -f ../pair_eam_alloy_cuda.h
   rm -f ../pair_eam_cuda.h
   rm -f ../pair_eam_fs_cuda.h
   rm -f ../pair_gran_hooke_cuda.h
   rm -f ../pair_lj96_cut_cuda.h
   rm -f ../pair_lj_charmm_coul_charmm_cuda.h
   rm -f ../pair_lj_charmm_coul_charmm_implicit_cuda.h
   rm -f ../pair_lj_charmm_coul_long_cuda.h
   rm -f ../pair_lj_class2_coul_cut_cuda.h
   rm -f ../pair_lj_class2_coul_long_cuda.h
   rm -f ../pair_lj_class2_cuda.h
   rm -f ../pair_lj_cut_coul_cut_cuda.h
   rm -f ../pair_lj_cut_coul_debye_cuda.h
   rm -f ../pair_lj_cut_coul_long_cuda.h
   rm -f ../pair_lj_cut_cuda.h
   rm -f ../pair_lj_cut_experimental_cuda.h
   rm -f ../pair_lj_expand_cuda.h
   rm -f ../pair_lj_gromacs_coul_gromacs_cuda.h
   rm -f ../pair_lj_gromacs_cuda.h
   rm -f ../pair_lj_smooth_cuda.h
   rm -f ../pair_morse_cuda.h
   rm -f ../pppm_cuda.h
   rm -f ../verlet_cuda.h
 
   rm -f ../pair_sw_cuda.h 
   rm -f ../pair_sw_cuda.cpp
   rm -f ../pair_tersoff_cuda.h 
   rm -f ../pair_tersoff_cuda.cpp 
   rm -f ../pair_tersoff_zbl_cuda.h 
   rm -f ../pair_tersoff_zbl_cuda.cpp   
   
   rm -f ../cuda.h
   rm -f ../cuda_data.h
   rm -f ../cuda_modify_flags.h
   rm -f ../cuda_neigh_list.h
 fi
diff --git a/src/USER-MOLFILE/Install.sh b/src/USER-MOLFILE/Install.sh
index 7bcb61041..12280e0fd 100644
--- a/src/USER-MOLFILE/Install.sh
+++ b/src/USER-MOLFILE/Install.sh
@@ -1,51 +1,51 @@
 # Install/unInstall package files in LAMMPS
 
 if (test $1 = 1) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*molfile[^ \t]* //' ../Makefile.package
     sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(molfile_SYSINC) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(molfile_SYSLIB) |' ../Makefile.package
     sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(molfile_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*USER-MOLFILE.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
-    sed -i '4 i \
-include ..\/USER-MOLFILE\/Makefile.lammps\
+    sed -i -e '4 i \
+include ..\/USER-MOLFILE\/Makefile.lammps
 ' ../Makefile.package.settings
   fi
 
   cp molfile_interface.cpp ..
   cp dump_molfile.cpp ..
   cp reader_molfile.cpp ..
 
   cp molfile_interface.h ..
   cp dump_molfile.h ..
   cp reader_molfile.h ..
 
   cp molfile_plugin.h ..
   cp vmdplugin.h ..
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
     sed -i -e 's/[^ \t]*molfile[^ \t]* //' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/^include.*USER-MOLFILE.*$/d' ../Makefile.package.settings
   fi
 
   rm -f ../molfile_interface.cpp
   rm -f ../dump_molfile.cpp
   rm -f ../reader_molfile.cpp
 
   rm -f ../molfile_interface.h
   rm -f ../dump_molfile.h
   rm -f ../reader_molfile.h
 
   rm -f ../molfile_plugin.h
   rm -f ../vmdplugin.h
 fi