Update to Make file and working compile

src/Makefile

@@ -1,53 +1,49 @@
-FC=gfortran
-
-#Ifort flags
-#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
-
-#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
-
-#gfortran flags
-FFLAGS=-mcmodel=large -O3 -g
-#FFLAGS=-mcmodel=large -O0 -g -fbacktrace -fcheck=all
-
-MODES=mode_create.o mode_merge.o mode_convert.o mode_metric.o mode_calc.o
-OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o opt_redef_box.o opt_slip_plane.o
-OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o neighbors.o $(MODES) $(OPTIONS) call_option.o sorts.o
-
-.SUFFIXES:
 .SUFFIXES: .c .f .f90 .F90 .o
+.DEFAULT_GOAL := all
 
-cacmb: $(OBJECTS) 
-	$(FC) $(FFLAGS) $(OBJECTS) parameters.o -o $@
+FC=mpif90
+FFLAGS=-Wall -mcmodel=large -O0 -g -fbacktrace -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow,denormal 
+
+OBJDIR=obj
+SRCS := $(wildcard *.f90)
+OBJECTS := $(addprefix $(OBJDIR)/,$(SRCS:%.f90=%.o))
+
+
+
+#----------------- DEPENDENCIES -----------------#
+# GENERATED USING https://github.com/ZedThree/fort_depend.py **requires python3**
+# > pip install fortdepend
+# > fortdepend -o Makefile.dep -i mpi -b obj/
+include Makefile.dep
+
+#----------------- DEFAULTS -----------------#
+all: cacmb
+
+.PHONY: deps
+cacmb: $(OBJECTS) $(OBJDIR)/main.o
+	$(FC) $(FFLAGS) $(OBJECTS) -o $@
+
+$(OBJDIR)/%.o: %.f90
+	@mkdir -p $(@D)
+	$(FC) $(FFLAGS) -c -o $@ $< -J$(OBJDIR)
 
 .f90.o: 
 	$(FC) $(FFLAGS) -c $< 
 
+
+deps:
+	@fortdepend -o Makefile.dep -i mpi -b obj -w
+
+#----------------- CLEAN UP -----------------#
+
 .PHONY: clean
-clean: 
-	$(RM) cacmb  *.o *.mod *genmod*
+clean:
+	$(RM) *.mod *.o
+	$(RM) $(OBJDIR)/*.mod $(OBJDIR)/*.o CAC
+	@$(RM) -rf obj/
 
-testfuncs: testfuncs.o functions.o subroutines.o
-	$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@
+.PHONY: clean-all
+clean-all: clean 
 
-.PHONY: cleantest
-cleantest:
-	$(RM) testfuncs testfuncs.o
-
-.PHONY: test
-test: testfuncs
-	./testfuncs
-
-.PHONY: install
-install: cacmb
-	cp ./cacmb /usr/local/bin
-
-$(OBJECTS) : parameters.o
-atoms.o subroutines.o testfuncs.o box.o : functions.o
-main.o io.o $(MODES) $(OPTIONS) : elements.o 
-call_mode.o : $(MODES)
-call_option.o : $(OPTIONS)
-elements.o : sorts.o
-$(MODES) $(OPTIONS) subroutines.o io.o : atoms.o box.o
-$(MODES) main.o : io.o
-testfuncs.o elements.o mode_create.o $(OPTIONS) $(MODES): subroutines.o
-opt_delete.o mode_metric.o : neighbors.o
+# DEBUGGING VARIABLE PRINT
+print-%  : ; @echo $* = $($*)