clean up all Makefiles:

- all objects now go in a dedicated dir
- to avoid error-prone repetitions, objects are put in env variables
- correct target mismatches that caused builds to be repeated even when not necessary

src/Makefile

 SUBDIRS := cluster sphere trapping
 SRCDIR=$(PWD)
+OBJDIR=$(SRCDIR)/objects
 BUILDDIR=$(SRCDIR)/../build
 DOCSDIR=$(SRCDIR)/../doc
 
@@ -12,14 +13,13 @@ $(SUBDIRS):
 	$(MAKE) -C $@
 
 clean:
-	rm -f $(BUILDDIR)/cluster/*.o
-	rm -f $(BUILDDIR)/sphere/*.o
-	rm -f $(BUILDDIR)/trapping/*.o
+	rm -f $(OBJDIR)/*.o
 
 wipe:
 	rm -f $(BUILDDIR)/cluster/*
 	rm -f $(BUILDDIR)/sphere/*
 	rm -f $(BUILDDIR)/trapping/*
+	rm -f $(OBJDIR)/*.o
 	if [ -d $(DOCSDIR)/build/html ]; then rm -r $(DOCSDIR)/build/html; fi
 	if [ -d $(DOCSDIR)/build/latex ]; then rm -r $(DOCSDIR)/build/latex; fi
 

src/cluster/Makefile

-BUILDDIR=../../build/cluster
+ifndef BUILDDIR
+override BUILDDIR=../../build/cluster
+endif
+ifndef OBJDIR
+override OBJDIR=../objects
+endif
 
 include ../make.inc
 
+F_CLU_OBJS=$(OBJDIR)/clu.o $(OBJDIR)/edfb_clu.o
 
-all: clu edfb_clu np_cluster
+CXX_CLU_OBJS=$(OBJDIR)/np_cluster.o $(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/Parsers.o $(OBJDIR)/sph_subs.o $(OBJDIR)/clu_subs.o $(OBJDIR)/cluster.o
 
-clu: clu.o
-	$(FC) $(FCFLAGS) -o $(BUILDDIR)/clu $(BUILDDIR)/clu.o $(LDFLAGS)
 
-edfb_clu: edfb_clu.o
-	$(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb_clu $(BUILDDIR)/edfb_clu.o $(LDFLAGS)
+all: $(BUILDDIR)/clu $(BUILDDIR)/edfb_clu $(BUILDDIR)/np_cluster
 
-np_cluster: $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o
-	$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_cluster $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o $(CXXLDFLAGS) 
+$(BUILDDIR)/clu: $(OBJDIR)/clu.o
+	$(FC) $(FCFLAGS) -o $(BUILDDIR)/clu $(OBJDIR)/clu.o $(LDFLAGS)
 
-#$(BUILDDIR)/np_cluster.o:
-#	$(CXX) $(CXXFLAGS) -c np_cluster.cpp -o $(BUILDDIR)/np_cluster.o
+$(BUILDDIR)/edfb_clu: $(OBJDIR)/edfb_clu.o
+	$(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb_clu $(OBJDIR)/edfb_clu.o $(LDFLAGS)
 
-#$(BUILDDIR)/Commons.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/Commons.cpp -o $(BUILDDIR)/Commons.o
-
-#$(BUILDDIR)/Configuration.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/Configuration.cpp -o $(BUILDDIR)/Configuration.o
-
-#$(BUILDDIR)/file_io.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/file_io.cpp -o $(BUILDDIR)/file_io.o
-
-#$(BUILDDIR)/Parsers.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/Parsers.cpp -o $(BUILDDIR)/Parsers.o
-
-#$(BUILDDIR)/cluster.o:
-#	$(CXX) $(CXXFLAGS) -c cluster.cpp -o $(BUILDDIR)/cluster.o
-
-#$(BUILDDIR)/clu_subs.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/clu_subs.cpp -o $(BUILDDIR)/clu_subs.o
-
-#$(BUILDDIR)/sph_subs.o:
-#	$(CXX) $(CXXFLAGS) -c ../libnptm/sph_subs.cpp -o $(BUILDDIR)/sph_subs.o
+$(BUILDDIR)/np_cluster: $(CXX_CLU_OBJS)
+	$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_cluster $(CXX_CLU_OBJS) $(CXXLDFLAGS) 
 
 clean:
-	rm -f $(BUILDDIR)/*.o
+	rm -f $(F_CLU_OBJS) $(CXX_CLU_OBJS)
 
 wipe:
-	rm -f $(BUILDDIR)/clu $(BUILDDIR)/edfb_clu $(BUILDDIR)/*.o
+	rm -f $(BUILDDIR)/clu $(BUILDDIR)/edfb_clu $(F_CLU_OBJS) $(CXX_CLU_OBJS)
 

src/make.inc

@@ -41,13 +41,16 @@ override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(LDFLAGS)
 endif
 
 %.o : %.f
-	$(FC) $(FCFLAGS) -c -o $(BUILDDIR)/$@ $<
+	$(FC) $(FCFLAGS) -c -o $(OBJDIR)/$@ $<
 
 %.o : %.cpp
-	$(CXX) $(CXXFLAGS) -c -o $(BUILDDIR)/$@ $<
+	$(CXX) $(CXXFLAGS) -c -o $(OBJDIR)/$@ $<
 
-$(BUILDDIR)/%.o : %.cpp
-	$(CXX) $(CXXFLAGS) -c -o $(BUILDDIR)/$@ $<
+$(OBJDIR)/%.o : %.f
+	$(FC) $(FCFLAGS) -c -o $(OBJDIR)/$@ $<
 
-$(BUILDDIR)/%.o : ../libnptm/%.cpp
-	$(CXX) $(CXXFLAGS) -c -o $(BUILDDIR)/$@ ../libnptm/$<
+$(OBJDIR)/%.o : %.cpp
+	$(CXX) $(CXXFLAGS) -c -o $(OBJDIR)/$@ $<
+
+$(OBJDIR)/%.o : ../libnptm/%.cpp
+	$(CXX) $(CXXFLAGS) -c -o $(OBJDIR)/$@ ../libnptm/$<