diff --git a/Makefile.am b/Makefile.am
index 407d10df0c18c1ddb070daa8e9aa625ea3cb13be..f777f20c02953a750e90ac8e7767e82377d52cff 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,22 +1,31 @@
ACLOCAL_AMFLAGS = -I m4
SUBDIRS =
+DIST_SUBDIRS =
if BUILD_S_OMP
SUBDIRS += sPuReMD
+DIST_SUBDIRS += sPuReMD
endif
if BUILD_MPI
SUBDIRS += PuReMD
+DIST_SUBDIRS += PuReMD
endif
if BUILD_GPU
SUBDIRS += PuReMD-GPU
+DIST_SUBDIRS += PuReMD-GPU
endif
if BUILD_MPI_GPU
SUBDIRS += PG-PuReMD
+DIST_SUBDIRS += PG-PuReMD
endif
if BUILD_DOC
SUBDIRS += doc
+DIST_SUBDIRS += doc
endif
-dist-hook: rm -rf `find $(distdir) -name .git`
+EXTRA_DIST = data environ tools
+
+dist-hook:
+ rm -rf `find $(distdir) -name .git`
diff --git a/PG-PuReMD/Makefile.am b/PG-PuReMD/Makefile.am
index 3d61101e8c97e13c640a7ba33c5ba82191dc4b8d..9c177cd81f429479040bd75dda2e3dc89601c0a0 100644
--- a/PG-PuReMD/Makefile.am
+++ b/PG-PuReMD/Makefile.am
@@ -28,6 +28,14 @@ bin_pg_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c
src/qEq.c src/bond_orders.c src/multi_body.c src/bonds.c src/valence_angles.c \
src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
src/integrate.c src/init_md.c src/parallelreax.c
+include_HEADERS = src/reax_defs.h src/reax_types.h \
+ src/allocate.h src/basic_comm.h src/ffield.h src/grid.h src/list.h \
+ src/lookup.h src/io_tools.h src/reset_tools.h src/restart.h src/random.h \
+ src/tool_box.h src/traj.h src/analyze.h src/box.h src/system_props.h \
+ src/control.h src/comm_tools.h src/geo_tools.h src/linear_solvers.h src/neighbors.h \
+ src/qEq.h src/bond_orders.h src/multi_body.h src/bonds.h src/valence_angles.h \
+ src/hydrogen_bonds.h src/torsion_angles.h src/nonbonded.h src/forces.h \
+ src/integrate.h src/init_md.h
bin_pg_puremd_LDADD = src/vector.o
if USE_CUDA
@@ -40,6 +48,15 @@ bin_pg_puremd_SOURCES += src/cuda_utils.cu src/dev_alloc.cu src/cuda_environment
src/cuda_qEq.cu src/cuda_linear_solvers.cu src/matvec.cu src/dual_matvec.cu \
src/cuda_nonbonded.cu src/cuda_integrate.cu src/cuda_post_evolve.cu \
src/cuda_init_md.cu src/validation.cu src/cuda_lookup.cu
+include_HEADERS += src/cuda_utils.h src/dev_alloc.h src/cuda_environment.h \
+ src/dev_system_props.h src/reduction.h src/center_mass.h \
+ src/cuda_copy.h src/cuda_reset_tools.h src/dev_list.h \
+ src/cuda_neighbors.h src/cuda_bond_orders.h src/cuda_bonds.h \
+ src/cuda_multi_body.h src/cuda_valence_angles.h \
+ src/cuda_torsion_angles.h src/cuda_hydrogen_bonds.h src/cuda_forces.h \
+ src/cuda_qEq.h src/cuda_linear_solvers.h src/matvec.h src/dual_matvec.h \
+ src/cuda_nonbonded.h src/cuda_integrate.h src/cuda_post_evolve.h \
+ src/cuda_init_md.h src/validation.h src/cuda_lookup.h
# dummy source to cause C linking
nodist_EXTRA_bin_pg_puremd_SOURCES = src/dummy.c
diff --git a/PuReMD-GPU/Makefile.am b/PuReMD-GPU/Makefile.am
index cc3b6a94f98b762b5fef91e39f6675adf28733ca..e2d60f76f7d9387b70b1566223a766a9027dd590 100644
--- a/PuReMD-GPU/Makefile.am
+++ b/PuReMD-GPU/Makefile.am
@@ -28,6 +28,18 @@ bin_puremd_gpu_SOURCES = src/analyze.c src/print_utils.c src/reset_utils.c src/p
src/cuda_utils.cu src/cuda_copy.cu src/cuda_init.cu src/reduction.cu \
src/center_mass.cu src/helpers.cu src/validation.cu src/matvec.cu
+include_HEADERS = src/mytypes.h src/analyze.h src/print_utils.h \
+ src/reset_utils.h src/param.h src/pdb_tools.h \
+ src/GMRES.h src/QEq.h src/allocate.h src/bond_orders.h \
+ src/box.h src/forces.h src/four_body_interactions.h \
+ src/grid.h src/init_md.h src/integrate.h src/list.h \
+ src/lookup.h src/neighbors.h \
+ src/restart.h src/single_body_interactions.h \
+ src/system_props.h src/three_body_interactions.h \
+ src/traj.h src/two_body_interactions.h src/vector.h \
+ src/cuda_utils.h src/cuda_copy.h src/cuda_init.h src/reduction.h \
+ src/center_mass.h src/helpers.h src/validation.h src/matvec.h
+
# dummy source to cause C linking
nodist_EXTRA_bin_puremd_gpu_SOURCES = src/dummy.c
diff --git a/PuReMD/Makefile.am b/PuReMD/Makefile.am
index 6c248d2378875ab0000bb0936f316958255f3ce4..17643df14cf731708227a6aeec1f38fb92756740 100644
--- a/PuReMD/Makefile.am
+++ b/PuReMD/Makefile.am
@@ -8,5 +8,13 @@ bin_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src
src/bonds.c src/valence_angles.c src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
src/integrate.c src/init_md.c src/parallelreax.c
+include_HEADERS = src/reax_defs.h src/reax_types.h \
+ src/allocate.h src/basic_comm.h src/ffield.h src/grid.h src/list.h src/lookup.h \
+ src/io_tools.h src/reset_tools.h src/restart.h src/random.h src/tool_box.h src/traj.h \
+ src/vector.h src/analyze.h src/box.h src/system_props.h src/control.h src/comm_tools.h \
+ src/geo_tools.h src/linear_solvers.h src/neighbors.h src/qEq.h src/bond_orders.h src/multi_body.h \
+ src/bonds.h src/valence_angles.h src/hydrogen_bonds.h src/torsion_angles.h src/nonbonded.h src/forces.h \
+ src/integrate.h src/init_md.h
+
bin_puremd_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS)
bin_puremd_LDFLAGS = $(AM_LDFLAGS) $(MPI_LDFLAGS)
diff --git a/configure.ac b/configure.ac
index a75256843d41ae4d1d47ac275e147b020aff39ed..11130d749c8ffc2399186535235bde1a7d188c5e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -143,14 +143,16 @@ then
export BUILD_SUPERLU_MT="${package_superlu_mt}"
fi
+AC_ARG_ENABLE([doc],
+ [AS_HELP_STRING([--enable-doc],
+ [enable documentation generation @<:@default: no@:>@])],
+ [pack_doc_enabled=${enableval}], [pack_doc_enabled=no])
AC_PROG_PDFLATEX
-AM_CONDITIONAL([BUILD_DOC], [test "x${PDFLATEX}" != "x"])
+AM_CONDITIONAL([BUILD_DOC], [test "x${pack_doc_enabled}" = "xyes" && test "x${PDFLATEX}" != "x"])
+if test "x${pack_doc_enabled}" = "xyes"; then
+ AC_CONFIG_SUBDIRS([doc])
+fi
AC_CONFIG_FILES([Makefile])
-if test "x${PDFLATEX}" != "x"
-then
- AC_CONFIG_FILES([doc/Makefile])
-fi
-
AC_OUTPUT
diff --git a/sPuReMD/Makefile.am b/sPuReMD/Makefile.am
index 22bfb4986956b78797bc6ceccbb4bbd64aabed72..e4f0c7b9f938780377e23cf495868d6f572833fa 100644
--- a/sPuReMD/Makefile.am
+++ b/sPuReMD/Makefile.am
@@ -8,3 +8,11 @@ bin_spuremd_SOURCES = src/ffield.c src/grid.c src/list.c src/lookup.c src/print_
src/single_body_interactions.c src/two_body_interactions.c \
src/three_body_interactions.c src/four_body_interactions.c src/forces.c \
src/integrate.c src/init_md.c src/testmd.c
+
+include_HEADERS = src/mytypes.h src/ffield.h src/grid.h src/list.h src/lookup.h src/print_utils.h \
+ src/reset_utils.h src/restart.h src/random.h src/tool_box.h src/traj.h \
+ src/vector.h src/allocate.h src/analyze.h src/box.h src/system_props.h src/control.h \
+ src/geo_tools.h src/neighbors.h src/GMRES.h src/QEq.h src/bond_orders.h \
+ src/single_body_interactions.h src/two_body_interactions.h \
+ src/three_body_interactions.h src/four_body_interactions.h src/forces.h \
+ src/integrate.h src/init_md.h