diff --git a/lib/atc/Makefile.g++ b/lib/atc/Makefile.g++
index d15e6cb3b8..bb3028392a 100644
--- a/lib/atc/Makefile.g++
+++ b/lib/atc/Makefile.g++
@@ -1,3 +1,4 @@
+# library build -*- makefile -*-
 SHELL = /bin/sh
 
 # which file will be copied to Makefile.lammps
@@ -5,6 +6,7 @@ SHELL = /bin/sh
 EXTRAMAKE = Makefile.lammps.installed
 
 # ------ FILES ------
+
 SRC = $(wildcard *.cpp)
 INC = $(wildcard *.h)
 
@@ -47,5 +49,9 @@ DEPENDS = $(OBJ:.o=.d)
 
 # ------ CLEAN ------
 
+.PHONY: clean lib
+
 clean:
 	-rm *.o *.d *~ $(LIB)
+
+sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.lammps b/lib/atc/Makefile.lammps
deleted file mode 100644
index c8cd66af26..0000000000
--- a/lib/atc/Makefile.lammps
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-user-atc_SYSINC =
-user-atc_SYSLIB = -lblas -llapack
-user-atc_SYSPATH =
diff --git a/lib/atc/Makefile.mingw32-cross b/lib/atc/Makefile.mingw32-cross
deleted file mode 100644
index 8b33540981..0000000000
--- a/lib/atc/Makefile.mingw32-cross
+++ /dev/null
@@ -1,67 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		i686-w64-mingw32-g++
-CCFLAGS =	-I../../src -I../../src/STUBS -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-                -ffast-math -funroll-loops -fstrict-aliasing 	\
-		-DLAMMPS_SMALLSMALL -Wno-uninitialized
-ARCHIVE =	i686-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw32-cross-mpi b/lib/atc/Makefile.mingw32-cross-mpi
deleted file mode 100644
index c5feeca81a..0000000000
--- a/lib/atc/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,68 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32-mpi/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		i686-w64-mingw32-g++
-CCFLAGS =	-I../../tools/mingw-cross/mpich2-win32/include/		\
-		-I../../src -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-                -ffast-math -funroll-loops -fstrict-aliasing 	\
-		-DLAMMPS_SMALLSMALL -Wno-uninitialized
-ARCHIVE =	i686-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw64-cross b/lib/atc/Makefile.mingw64-cross
deleted file mode 100644
index fbd3a02610..0000000000
--- a/lib/atc/Makefile.mingw64-cross
+++ /dev/null
@@ -1,67 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		  x86_64-w64-mingw32-g++
-CCFLAGS =	-I../../src -I../../src/STUBS -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-		-DLAMMPS_SMALLBIG -Wno-uninitialized
-ARCHIVE =	x86_64-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw64-cross-mpi b/lib/atc/Makefile.mingw64-cross-mpi
deleted file mode 100644
index f8dd64eae3..0000000000
--- a/lib/atc/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,68 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64-mpi/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		  x86_64-w64-mingw32-g++
-CCFLAGS =	-I../../tools/mingw-cross/mpich2-win64/include/		\
-		-I../../src -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-		-DLAMMPS_SMALLBIG -Wno-uninitialized
-ARCHIVE =	x86_64-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mpic++ b/lib/atc/Makefile.mpi
similarity index 59%
rename from lib/atc/Makefile.mpic++
rename to lib/atc/Makefile.mpi
index c9dfdb79c9..ec941efdcb 100644
--- a/lib/atc/Makefile.mpic++
+++ b/lib/atc/Makefile.mpi
@@ -2,38 +2,54 @@
 SHELL = /bin/sh
 
 # which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.installed
+EXTRAMAKE = Makefile.lammps.linalg
+
 # ------ FILES ------
+
 SRC = $(wildcard *.cpp)
 INC = $(wildcard *.h)
+
 # ------ DEFINITIONS ------
+
 LIB = libatc.a
 OBJ =   $(SRC:.cpp=.o)
+
+default: lib
+
 # ------ SETTINGS ------
 
+.PHONY: clean lib depend
+
 # include any MPI settings needed for the ATC library to build with
 # must be the same MPI library that LAMMPS is built with
 
-CC =	        mpic++
-CCFLAGS =       -O3 -Wall -g -I../../src -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+CC =	        mpicxx
+CCFLAGS =       -O3 -Wall -g -fPIC
+CPPFLAGS = -I../../src -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
 ARCHIVE =	ar
 ARCHFLAG =	-rc
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
 # ------ MAKE PROCEDURE ------
+
 lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps
+
 # ------ COMPILE RULES ------
+
 %.o:%.cpp
-	$(CC) $(CCFLAGS) -c $<
-%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+	$(CC) $(CPPFLAGS) $(CCFLAGS) -c $<
+
 # ------ DEPENDENCIES ------
-DEPENDS = $(OBJ:.o=.d)
+
+depend .depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(INCFLAGS) -- $^ > .depend || exit 1
+
+fastdep.exe: ../../src/DEPEND/fastdep.c
+	@cc -O -o $@ $<
+
 # ------ CLEAN ------
+
 clean:
-	-rm *.o *.d *~ $(LIB)
+	-rm -f *.o *~ .depend $(LIB) fastdep.exe
 
 sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.serial b/lib/atc/Makefile.serial
index 44ce5fd341..70b786a6b8 100644
--- a/lib/atc/Makefile.serial
+++ b/lib/atc/Makefile.serial
@@ -14,18 +14,20 @@ INC = $(wildcard *.h)
 LIB = libatc.a
 OBJ =   $(SRC:.cpp=.o)
 
+default: lib
+
 # ------ SETTINGS ------
 
+.PHONY: clean lib depend
+
 # include any MPI settings needed for the ATC library to build with
 # must be the same MPI library that LAMMPS is built with
 
 CC =	        g++
-CCFLAGS =       -O -g -fPIC -I../../src -I../../src/STUBS
+CCFLAGS =       -O3 -g -fPIC
+CPPFLAGS = -I../../src -I../../src/STUBS
 ARCHIVE =	ar
 ARCHFLAG =	-rc
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
 # ------ MAKE PROCEDURE ------
 
 lib: 	$(OBJ)
@@ -35,17 +37,19 @@ lib: 	$(OBJ)
 # ------ COMPILE RULES ------
 
 %.o:%.cpp
-	$(CC) $(CCFLAGS) -c $<
-%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+	$(CC) $(CPPFLAGS) $(CCFLAGS) -c $<
 
 # ------ DEPENDENCIES ------
 
-DEPENDS = $(OBJ:.o=.d)
+depend .depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(INCFLAGS) -- $^ > .depend || exit 1
+
+fastdep.exe: ../../src/DEPEND/fastdep.c
+	@cc -O -o $@ $<
 
 # ------ CLEAN ------
 
 clean:
-	-rm *.o *.d *~ $(LIB)
+	-rm -f *.o *~ .depend $(LIB) fastdep.exe
 
-sinclude $(DEPENDS)
+sinclude .depend
diff --git a/lib/awpmd/Makefile.mingw32-cross b/lib/awpmd/Makefile.mingw32-cross
deleted file mode 100644
index 6a93987173..0000000000
--- a/lib/awpmd/Makefile.mingw32-cross
+++ /dev/null
@@ -1,80 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = logexc.cpp wpmd.cpp wpmd_split.cpp
-vpath %.cpp ivutils/src
-vpath %.cpp systems/interact/TCP
-
-INC = \
-    cerf.h \
-    cerf2.h \
-    cerf_octave.h \
-    cvector_3.h \
-    lapack_inter.h \
-    logexc.h \
-    pairhash.h \
-    refobj.h \
-    tcpdefs.h \
-    vector_3.h \
-    wavepacket.h \
-    wpmd.h \
-    wpmd_split.h
-
-# ------ DEFINITIONS ------
-DIR = Obj_mingw32/
-LIB = $(DIR)libawpmd.a
-OBJ =  $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =	  i686-w64-mingw32-g++
-CCFLAGS = 	-O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-		-finline-functions		\
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
-ARCHIVE =	i686-w64-mingw32-ar
-ARCHFLAG =	-rscv
-DEPFLAGS =  -M
-#LINK =         
-#LINKFLAGS =	
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): 	$(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mingw32-cross-mpi b/lib/awpmd/Makefile.mingw32-cross-mpi
deleted file mode 100644
index cc2a76111a..0000000000
--- a/lib/awpmd/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw32-cross
-	rm -f Obj_mingw32-mpi
-	ln -s Obj_mingw32 Obj_mingw32-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	rm -f Obj_mingw32-mpi
-
diff --git a/lib/awpmd/Makefile.mingw64-cross b/lib/awpmd/Makefile.mingw64-cross
deleted file mode 100644
index 1f3e608129..0000000000
--- a/lib/awpmd/Makefile.mingw64-cross
+++ /dev/null
@@ -1,79 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = logexc.cpp wpmd.cpp wpmd_split.cpp
-vpath %.cpp ivutils/src
-vpath %.cpp systems/interact/TCP
-
-INC = \
-    cerf.h \
-    cerf2.h \
-    cerf_octave.h \
-    cvector_3.h \
-    lapack_inter.h \
-    logexc.h \
-    pairhash.h \
-    refobj.h \
-    tcpdefs.h \
-    vector_3.h \
-    wavepacket.h \
-    wpmd.h \
-    wpmd_split.h
-
-# ------ DEFINITIONS ------
-DIR = Obj_mingw64/
-LIB = $(DIR)libawpmd.a
-OBJ =  $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =	  x86_64-w64-mingw32-g++
-CCFLAGS =  -O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
-ARCHIVE =	x86_64-w64-mingw32-ar
-ARCHFLAG =	-rscv
-DEPFLAGS =  -M
-#LINK =         
-#LINKFLAGS =	
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): 	$(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mingw64-cross-mpi b/lib/awpmd/Makefile.mingw64-cross-mpi
deleted file mode 100644
index 1ec1a0995b..0000000000
--- a/lib/awpmd/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw64-cross
-	rm -f Obj_mingw64-mpi
-	ln -s Obj_mingw64 Obj_mingw64-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	rm -f Obj_mingw64-mpi
-
diff --git a/lib/h5md/Makefile.mpi b/lib/h5md/Makefile.mpi
new file mode 120000
index 0000000000..df682a9547
--- /dev/null
+++ b/lib/h5md/Makefile.mpi
@@ -0,0 +1 @@
+Makefile.h5cc
\ No newline at end of file
diff --git a/lib/h5md/Makefile.serial b/lib/h5md/Makefile.serial
new file mode 120000
index 0000000000..df682a9547
--- /dev/null
+++ b/lib/h5md/Makefile.serial
@@ -0,0 +1 @@
+Makefile.h5cc
\ No newline at end of file