diff --git a/GFDL_tools/Makefile.am b/GFDL_tools/Makefile.am
new file mode 100644
index 000000000..16862b750
--- /dev/null
+++ b/GFDL_tools/Makefile.am
@@ -0,0 +1,33 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./GFDL_tools.
+#
+# Ed Hartnett 2019-09-10
+
+# Build these uninstalled convenience libraries.
+noinst_LTLIBRARIES = libread_climate_nudge_data.la libfv_cmip_diag.la \
+libfv_climate_nudge.la libfv_ada_nudge.la
+
+# Each convenience library depends on its source.
+libread_climate_nudge_data_la_SOURCES = read_climate_nudge_data.F90
+libfv_cmip_diag_la_SOURCES = fv_cmip_diag.F90
+libfv_climate_nudge_la_SOURCES = fv_climate_nudge.F90
+libfv_ada_nudge_la_SOURCES = fv_ada_nudge.F90
+
+# Each mod file depends on the .o file.
+read_climate_nudge_data_mod.mod: read_climate_nudge_data.$(OBJEXT)
+fv_cmip_diag_mod.mod: fv_cmip_diag.$(OBJEXT)
+fv_climate_nudge_mod.mod: fv_climate_nudge.$(OBJEXT)
+fv_ada_nudge_mod.mod: fv_ada_nudge.$(OBJEXT)
+
+# Some mods are dependant on other mods in this dir.
+fv_climate_nudge.$(OBJEXT): read_climate_nudge_data_mod.mod
+
+# Mod files are built and then installed as headers.
+MODFILES = read_climate_nudge_data_mod.mod fv_cmip_diag_mod.mod \
+fv_climate_nudge_mod.mod fv_ada_nudge_mod.mod
+include_HEADERS = $(MODFILES)
+BUILT_SOURCES = $(MODFILES)
+
+EXTRA_DIST = 
+
+CLEANFILES = *.mod
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 000000000..d0e94d78e
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,11 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ..
+#
+# Ed Hartnett 2019-09-10
+
+# This directory stores libtool macros, put there by aclocal.
+ACLOCAL_AMFLAGS = -I m4
+
+# Run make targets in each of these subdirs
+SUBDIRS = GFDL_tools model_nh tools driver model
+
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 000000000..102db54ef
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,78 @@
+# This is the main configure file for the GFDL AM4
+# package.
+# Ed Hartnett 7/29/2019
+
+AC_PREREQ([2.59])
+
+# Initialize with name, version, and support email address.
+AC_INIT([AM4], [2.0-development], [])
+
+# Find out about the host we're building on.
+AC_CANONICAL_HOST
+
+# Find out about the target we're building for.
+AC_CANONICAL_TARGET
+
+AM_INIT_AUTOMAKE([foreign dist-zip subdir-objects])
+
+# Keep libtool macros in an m4 directory.
+AC_CONFIG_MACRO_DIR([m4])
+
+# Set up libtool.
+LT_PREREQ([2.4])
+LT_INIT()
+
+# Find the C compiler.
+AC_PROG_CC
+AM_PROG_CC_C_O
+AC_C_CONST
+AC_PROG_CPP
+
+# Find the Fortran compiler.
+AC_PROG_FC
+AC_PROG_F77
+
+# Find the install program.
+AC_PROG_INSTALL
+
+# Check to see if any macros must be set to enable large (>2GB) files.
+AC_SYS_LARGEFILE
+
+# Require MPI.
+AC_CHECK_FUNC([MPI_Init], [], [AC_MSG_ERROR([MPI C library required])])
+
+# Require FMS. But this does not work because fms_platform.h is
+# actually a fortran file, and AC_SEARCH_LIBS does not work with
+# fortran mod files. I will swing round to this again, until then
+# include the FMS library in FCFLAGS, LDFLAGS and LIBS.
+# AC_CHECK_HEADERS([fms_platform.h], [], [AC_MSG_ERROR([Can't find fms_platform.h.])])
+# AC_SEARCH_LIBS([__mpp_mod_MOD_mpp_init], [FMS], [],
+#                            [AC_MSG_ERROR([Can't find or link to the FMS Fortran library, set CPPFLAGS/LDFLAGS.])])
+
+
+# Check for netCDF C library.
+AC_SEARCH_LIBS([nc_create], [netcdf], [],
+                            [AC_MSG_ERROR([Can't find or link to the netcdf C library, set CPPFLAGS/LDFLAGS.])])
+
+# Check for netCDF Fortran library.
+AC_LANG_PUSH(Fortran)
+AC_SEARCH_LIBS([nf_create], [netcdff], [],
+                            [AC_MSG_ERROR([Can't find or link to the netcdf Fortran library, set CPPFLAGS/LDFLAGS.])])
+AC_LANG_POP(Fortran)
+
+# These defines are required for the build.
+#AC_DEFINE([use_netCDF], [1])
+#AC_DEFINE([use_libMPI], [1])
+#AC_DEFINE([SPMD], [1])
+
+# These files will be created when the configure script is run.
+AC_CONFIG_FILES([Makefile
+        GFDL_tools/Makefile
+        model_nh/Makefile
+        tools/Makefile
+        driver/Makefile
+        driver/GFDL/Makefile
+        driver/SHiELD/Makefile
+        model/Makefile
+        ])
+AC_OUTPUT()
diff --git a/driver/GFDL/Makefile.am b/driver/GFDL/Makefile.am
new file mode 100644
index 000000000..ad40c4083
--- /dev/null
+++ b/driver/GFDL/Makefile.am
@@ -0,0 +1,24 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./driver/GFDL.
+#
+# Ed Hartnett 2019-09-10
+
+# Build these uninstalled convenience libraries.
+noinst_LTLIBRARIES = libatmosphere.la
+
+# Each convenience library depends on its source.
+libatmosphere_la_SOURCES = atmosphere.F90
+
+# Each mod file depends on the .o file.
+atmosphere_mod.mod: atmosphere.$(OBJEXT)
+
+# Some mods are dependant on other mods in this dir.
+
+# Mod files are built and then installed as headers.
+MODFILES = atmosphere_mod.mod
+include_HEADERS = $(MODFILES)
+BUILT_SOURCES = $(MODFILES)
+
+EXTRA_DIST = 
+
+CLEANFILES = *.mod
diff --git a/driver/Makefile.am b/driver/Makefile.am
new file mode 100644
index 000000000..8e2102b4e
--- /dev/null
+++ b/driver/Makefile.am
@@ -0,0 +1,8 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./driver.
+#
+# Ed Hartnett 2019-09-10
+
+# Run make targets in each of these subdirs
+SUBDIRS = GFDL SHiELD
+
diff --git a/driver/SHiELD/Makefile.am b/driver/SHiELD/Makefile.am
new file mode 100644
index 000000000..eaebf1b4f
--- /dev/null
+++ b/driver/SHiELD/Makefile.am
@@ -0,0 +1,30 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./driver/SHiELD.
+#
+# Ed Hartnett 2019-09-10
+
+# Build these uninstalled convenience libraries.
+noinst_LTLIBRARIES = libatmosphere.la libconstants.la liblin_cloud_microphys.la
+
+# Each convenience library depends on its source.
+libatmosphere_la_SOURCES = atmosphere.F90
+libconstants_la_SOURCES = constants.F90
+liblin_cloud_microphys_la_SOURCES = lin_cloud_microphys.F90
+
+# Each mod file depends on the .o file.
+atmosphere_mod.mod: atmosphere.$(OBJEXT)
+constants_mod.mod: constants.$(OBJEXT)
+lin_cloud_microphys_mod.mod: lin_cloud_microphys.$(OBJEXT)
+
+# Some mods are dependant on other mods in this dir.
+atmosphere.$(OBJEXT): constants_mod.mod
+lin_cloud_microphys.$(OBJEXT): constants_mod.mod
+
+# Mod files are built and then installed as headers.
+MODFILES = atmosphere_mod.mod constants_mod.mod lin_cloud_microphys_mod.mod
+include_HEADERS = $(MODFILES)
+BUILT_SOURCES = $(MODFILES)
+
+EXTRA_DIST = 
+
+CLEANFILES = *.mod
diff --git a/model/Makefile.am b/model/Makefile.am
new file mode 100644
index 000000000..57c484392
--- /dev/null
+++ b/model/Makefile.am
@@ -0,0 +1,78 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./model.
+#
+# Ed Hartnett 2019-09-10
+
+# Build these uninstalled convenience libraries.
+noinst_LTLIBRARIES = libtp_core.la libboundary.la libfv_current_grid.la libfv_arrays.la \
+libfv_fill.la libfv_tracer2d.la libsw_core.la libfv_grid_utils.la \
+libfv_mapz.la libfv_control.la libfv_nesting.la libdyn_core.la \
+libfv_dynamics.la libfv_update_phys.la liba2b_edge.la libfv_sg.la \
+libfv_cmp.la
+
+# Each convenience library depends on its source.
+libtp_core_la_SOURCES = tp_core.F90
+libboundary_la_SOURCES = boundary.F90
+libfv_current_grid_la_SOURCES = fv_current_grid.F90
+libfv_arrays_la_SOURCES = fv_arrays.F90
+libfv_fill_la_SOURCES = fv_fill.F90
+libfv_tracer2d_la_SOURCES = fv_tracer2d.F90
+libsw_core_la_SOURCES = sw_core.F90
+libfv_grid_utils_la_SOURCES = fv_grid_utils.F90
+libfv_mapz_la_SOURCES = fv_mapz.F90
+libfv_control_la_SOURCES = fv_control.F90
+libfv_nesting_la_SOURCES = fv_nesting.F90
+libdyn_core_la_SOURCES = dyn_core.F90
+libfv_dynamics_la_SOURCES = fv_dynamics.F90
+libfv_update_phys_la_SOURCES = fv_update_phys.F90
+liba2b_edge_la_SOURCES = a2b_edge.F90
+libfv_sg_la_SOURCES = fv_sg.F90
+libfv_cmp_la_SOURCES = fv_cmp.F90
+
+# Each mod file depends on the .o file.
+tp_core_mod.mod: tp_core.$(OBJEXT)
+boundary_mod.mod: boundary.$(OBJEXT)
+fv_current_grid_mod.mod: fv_current_grid.$(OBJEXT)
+fv_arrays_mod.mod: fv_arrays.$(OBJEXT)
+fv_fill_mod.mod: fv_fill.$(OBJEXT)
+fv_tracer2d_mod.mod: fv_tracer2d.$(OBJEXT)
+sw_core_mod.mod: sw_core.$(OBJEXT)
+fv_grid_utils_mod.mod: fv_grid_utils.$(OBJEXT)
+fv_mapz_mod.mod: fv_mapz.$(OBJEXT)
+fv_control_mod.mod: fv_control.$(OBJEXT)
+fv_nesting_mod.mod: fv_nesting.$(OBJEXT)
+dyn_core_mod.mod: dyn_core.$(OBJEXT)
+fv_dynamics_mod.mod: fv_dynamics.$(OBJEXT)
+fv_update_phys_mod.mod: fv_update_phys.$(OBJEXT)
+a2b_edge_mod.mod: a2b_edge.$(OBJEXT)
+fv_sg_mod.mod: fv_sg.$(OBJEXT)
+fv_cmp_mod.mod: fv_cmp.$(OBJEXT)
+
+# Some mods are dependant on other mods in this dir.
+tp_core.$(OBJEXT): fv_arrays_mod.mod fv_grid_utils_mod.mod
+boundary.$(OBJEXT): fv_arrays_mod.mod
+fv_current_grid.$(OBJEXT): fv_arrays_mod.mod
+fv_tracer2d.$(OBJEXT): tp_core_mod.mod boundary_mod.mod fv_arrays_mod.mod
+sw_core.$(OBJEXT): tp_core_mod.mod fv_arrays_mod.mod a2b_edge_mod.mod
+fv_grid_utils.$(OBJEXT): fv_arrays_mod.mod
+fv_mapz.$(OBJEXT): fv_arrays_mod.mod fv_fill_mod.mod fv_grid_utils_mod.mod fv_cmp_mod.mod
+fv_control.$(OBJEXT): fv_arrays_mod.mod fv_grid_utils_mod.mod
+fv_nesting.$(OBJEXT): boundary_mod.mod fv_arrays_mod.mod sw_core_mod.mod fv_grid_utils_mod.mod fv_mapz_mod.mod fv_sg_mod.mod
+dyn_core.$(OBJEXT): tp_core_mod.mod boundary_mod.mod fv_arrays_mod.mod sw_core_mod.mod fv_update_phys_mod.mod a2b_edge_mod.mod
+fv_dynamics.$(OBJEXT): boundary_mod.mod fv_arrays_mod.mod fv_fill_mod.mod fv_tracer2d_mod.mod fv_grid_utils_mod.mod fv_mapz_mod.mod fv_nesting_mod.mod dyn_core_mod.mod fv_sg_mod.mod
+fv_update_phys.$(OBJEXT): boundary_mod.mod fv_arrays_mod.mod fv_grid_utils_mod.mod fv_mapz_mod.mod
+a2b_edge.$(OBJEXT): fv_arrays_mod.mod fv_grid_utils_mod.mod
+fv_cmp.$(OBJEXT): fv_arrays_mod.mod
+
+# Mod files are built and then installed as headers.
+MODFILES = tp_core_mod.mod boundary_mod.mod fv_current_grid_mod.mod \
+fv_arrays_mod.mod fv_fill_mod.mod fv_tracer2d_mod.mod sw_core_mod.mod \
+fv_grid_utils_mod.mod fv_mapz_mod.mod fv_control_mod.mod \
+fv_nesting_mod.mod dyn_core_mod.mod fv_dynamics_mod.mod \
+fv_update_phys_mod.mod a2b_edge_mod.mod fv_sg_mod.mod fv_cmp_mod.mod
+include_HEADERS = $(MODFILES)
+BUILT_SOURCES = $(MODFILES)
+
+EXTRA_DIST = 
+
+CLEANFILES = *.mod
diff --git a/model_nh/Makefile.am b/model_nh/Makefile.am
new file mode 100644
index 000000000..5d1a1eaec
--- /dev/null
+++ b/model_nh/Makefile.am
@@ -0,0 +1,27 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./model_nh.
+#
+# Ed Hartnett 2019-09-10
+
+# Build these uninstalled convenience libraries.
+noinst_LTLIBRARIES = libnh_utils.la libnh_core.la
+
+# Each convenience library depends on its source.
+libnh_utils_la_SOURCES = nh_utils.F90
+libnh_core_la_SOURCES = nh_core.F90
+
+# Each mod file depends on the .o file.
+nh_utils_mod.mod: nh_utils.$(OBJEXT)
+nh_core_mod.mod: nh_core.$(OBJEXT)
+
+# Some mods are dependant on other mods in this dir.
+nh_core.$(OBJEXT): nh_utils_mod.mod
+
+# Mod files are built and then installed as headers.
+MODFILES = nh_utils_mod.mod nh_core_mod.mod
+include_HEADERS = $(MODFILES)
+BUILT_SOURCES = $(MODFILES)
+
+EXTRA_DIST = 
+
+CLEANFILES = *.mod
diff --git a/tools/Makefile.am b/tools/Makefile.am
new file mode 100644
index 000000000..07769cea5
--- /dev/null
+++ b/tools/Makefile.am
@@ -0,0 +1,75 @@
+# This is an automake file for the GFDL AM4 model.
+# This builds directory ./tools.
+#
+# Ed Hartnett 2019-09-10
+
+# Build these uninstalled convenience libraries.
+noinst_LTLIBRARIES = libfv_surf_map.la libexternal_ic.la libfv_restart.la \
+libfv_grid_tools.la libfv_eta.la libinit_hydro.la libsim_nc_mod.la \
+libsorted_index.la libfv_mp_mod.la libexternal_sst.la libfv_timing.la \
+libfv_diagnostics.la libfv_nudge.la libfv_nggps_diag.la libfv_io.la \
+libtest_cases.la
+
+# Each convenience library depends on its source.
+libfv_surf_map_la_SOURCES = fv_surf_map.F90
+libexternal_ic_la_SOURCES = external_ic.F90
+libfv_restart_la_SOURCES = fv_restart.F90
+libfv_grid_tools_la_SOURCES = fv_grid_tools.F90
+libfv_eta_la_SOURCES = fv_eta.F90
+libinit_hydro_la_SOURCES = init_hydro.F90
+libsim_nc_mod_la_SOURCES = sim_nc_mod.F90
+libsorted_index_la_SOURCES = sorted_index.F90
+libfv_mp_mod_la_SOURCES = fv_mp_mod.F90
+libexternal_sst_la_SOURCES = external_sst.F90
+libfv_timing_la_SOURCES = fv_timing.F90
+libfv_diagnostics_la_SOURCES = fv_diagnostics.F90
+libfv_nudge_la_SOURCES = fv_nudge.F90
+libfv_nggps_diag_la_SOURCES = fv_nggps_diag.F90
+libfv_io_la_SOURCES = fv_io.F90
+libtest_cases_la_SOURCES = test_cases.F90
+
+# Each mod file depends on the .o file.
+fv_surf_map_mod.mod: fv_surf_map.$(OBJEXT)
+external_ic_mod.mod: external_ic.$(OBJEXT)
+fv_restart_mod.mod: fv_restart.$(OBJEXT)
+fv_grid_tools_mod.mod: fv_grid_tools.$(OBJEXT)
+fv_eta_mod.mod: fv_eta.$(OBJEXT)
+init_hydro_mod.mod: init_hydro.$(OBJEXT)
+sim_nc_mod_mod.mod: sim_nc_mod.$(OBJEXT)
+sorted_index_mod.mod: sorted_index.$(OBJEXT)
+fv_mp_mod_mod.mod: fv_mp_mod.$(OBJEXT)
+external_sst_mod.mod: external_sst.$(OBJEXT)
+fv_timing_mod.mod: fv_timing.$(OBJEXT)
+fv_diagnostics_mod.mod: fv_diagnostics.$(OBJEXT)
+fv_nudge_mod.mod: fv_nudge.$(OBJEXT)
+fv_nggps_diag_mod.mod: fv_nggps_diag.$(OBJEXT)
+fv_io_mod.mod: fv_io.$(OBJEXT)
+test_cases_mod.mod: test_cases.$(OBJEXT)
+
+# Some mods are dependant on other mods in this dir.
+fv_surf_map.$(OBJEXT): fv_mp_mod_mod.mod fv_timing_mod.mod
+external_ic.$(OBJEXT): fv_surf_map_mod.mod fv_eta_mod.mod init_hydro_mod.mod sim_nc_mod_mod.mod fv_mp_mod_mod.mod external_sst_mod.mod fv_timing_mod.mod fv_diagnostics_mod.mod fv_io_mod.mod test_cases_mod.mod
+fv_restart.$(OBJEXT): fv_surf_map_mod.mod external_ic_mod.mod fv_eta_mod.mod init_hydro_mod.mod fv_mp_mod_mod.mod fv_timing_mod.mod fv_diagnostics_mod.mod fv_io_mod.mod test_cases_mod.mod
+fv_grid_tools.$(OBJEXT): sorted_index_mod.mod fv_mp_mod_mod.mod fv_timing_mod.mod
+fv_eta.$(OBJEXT): fv_mp_mod_mod.mod
+init_hydro.$(OBJEXT): fv_mp_mod_mod.mod fv_diagnostics_mod.mod
+fv_timing.$(OBJEXT): fv_mp_mod_mod.mod
+fv_diagnostics.$(OBJEXT): fv_surf_map_mod.mod fv_eta_mod.mod fv_mp_mod_mod.mod
+fv_nudge.$(OBJEXT): sim_nc_mod_mod.mod fv_mp_mod_mod.mod external_sst_mod.mod fv_timing_mod.mod fv_diagnostics_mod.mod
+fv_nggps_diag.$(OBJEXT): fv_diagnostics_mod.mod
+fv_io.$(OBJEXT): fv_eta_mod.mod fv_mp_mod_mod.mod external_sst_mod.mod
+test_cases.$(OBJEXT): fv_surf_map_mod.mod fv_grid_tools_mod.mod fv_eta_mod.mod init_hydro_mod.mod fv_mp_mod_mod.mod fv_diagnostics_mod.mod
+
+# Mod files are built and then installed as headers.
+MODFILES = fv_surf_map_mod.mod external_ic_mod.mod fv_restart_mod.mod \
+fv_grid_tools_mod.mod fv_eta_mod.mod init_hydro_mod.mod \
+sim_nc_mod_mod.mod sorted_index_mod.mod fv_mp_mod_mod.mod \
+external_sst_mod.mod fv_timing_mod.mod fv_diagnostics_mod.mod \
+fv_nudge_mod.mod fv_nggps_diag_mod.mod fv_io_mod.mod \
+test_cases_mod.mod
+include_HEADERS = $(MODFILES)
+BUILT_SOURCES = $(MODFILES)
+
+EXTRA_DIST = 
+
+CLEANFILES = *.mod