Update to Make file and working compile

src/Makefile

@@ -1,53 +1,49 @@
-FC=gfortran
+.SUFFIXES: .c .f .f90 .F90 .o
+.DEFAULT_GOAL := all
 
-#Ifort flags
-#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
+FC=mpif90
+FFLAGS=-Wall -mcmodel=large -O0 -g -fbacktrace -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow,denormal 
 
-#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
+OBJDIR=obj
+SRCS := $(wildcard *.f90)
+OBJECTS := $(addprefix $(OBJDIR)/,$(SRCS:%.f90=%.o))
 
-#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
+#----------------- 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
 
-cacmb: $(OBJECTS) 
-	$(FC) $(FFLAGS) $(OBJECTS) parameters.o -o $@
+.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*
-
-testfuncs: testfuncs.o functions.o subroutines.o
-	$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@
-
-.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
+clean:
+	$(RM) *.mod *.o
+	$(RM) $(OBJDIR)/*.mod $(OBJDIR)/*.o CAC
+	@$(RM) -rf obj/
+
+.PHONY: clean-all
+clean-all: clean 
+
+# DEBUGGING VARIABLE PRINT
+print-%  : ; @echo $* = $($*)

src/Makefile.dep

@@ -0,0 +1,175 @@
+# This file is generated automatically. DO NOT EDIT!
+
+obj/main :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/caller.o \
+	obj/elements.o \
+	obj/functions.o \
+	obj/io.o \
+	obj/main.o \
+	obj/mode_calc.o \
+	obj/mode_check.o \
+	obj/mode_convert.o \
+	obj/mode_create.o \
+	obj/mode_merge.o \
+	obj/mode_metric.o \
+	obj/neighbors.o \
+	obj/opt_deform.o \
+	obj/opt_delete.o \
+	obj/opt_disl.o \
+	obj/opt_group.o \
+	obj/opt_orient.o \
+	obj/opt_redef_box.o \
+	obj/opt_slip_plane.o \
+	obj/parameters.o \
+	obj/sorts.o \
+	obj/subroutines.o
+
+obj/atoms.o :  \
+	obj/functions.o \
+	obj/parameters.o
+
+obj/box.o :  \
+	obj/functions.o \
+	obj/parameters.o
+
+obj/caller.o :  \
+	obj/box.o \
+	obj/mode_calc.o \
+	obj/mode_check.o \
+	obj/mode_convert.o \
+	obj/mode_create.o \
+	obj/mode_merge.o \
+	obj/mode_metric.o \
+	obj/opt_deform.o \
+	obj/opt_delete.o \
+	obj/opt_disl.o \
+	obj/opt_group.o \
+	obj/opt_orient.o \
+	obj/opt_redef_box.o \
+	obj/opt_slip_plane.o \
+	obj/parameters.o
+
+obj/elements.o :  \
+	obj/box.o \
+	obj/functions.o \
+	obj/parameters.o \
+	obj/sorts.o \
+	obj/subroutines.o
+
+obj/functions.o :  \
+	obj/parameters.o
+
+obj/io.o :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o
+
+obj/main.o :  \
+	obj/caller.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o
+
+obj/mode_calc.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_check.o :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/elements.o \
+	obj/functions.o \
+	obj/io.o \
+	obj/neighbors.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_convert.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o
+
+obj/mode_create.o :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_merge.o :  \
+	obj/atoms.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_metric.o :  \
+	obj/elements.o \
+	obj/io.o \
+	obj/neighbors.o \
+	obj/parameters.o
+
+obj/neighbors.o :  \
+	obj/elements.o \
+	obj/functions.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_deform.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_delete.o :  \
+	obj/elements.o \
+	obj/neighbors.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_disl.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_group.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_orient.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_redef_box.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/subroutines.o
+
+obj/opt_slip_plane.o :  \
+	obj/elements.o \
+	obj/functions.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/parameters.o : 
+
+obj/sorts.o :  \
+	obj/parameters.o
+
+obj/subroutines.o :  \
+	obj/box.o \
+	obj/functions.o \
+	obj/parameters.o

src/call_mode.f90

@@ -1,34 +0,0 @@
-subroutine call_mode(arg_pos)
-    !This code is used to parse the command line argument for the mode information and calls the required 
-    !mode module.
-
-    use mode_create
-    use mode_convert
-    use mode_merge
-    use mode_metric
-    use mode_calc
-    use parameters
-
-    implicit none    
-
-    integer, intent(out) :: arg_pos
-
-    select case(mode)
-    case('--create')
-        call create(arg_pos)
-    case('--convert')
-        call convert(arg_pos)  
-    case('--merge')
-        call merge(arg_pos) 
-    case('--metric')
-        call metric(arg_pos)
-    case('--calc')
-        call calc(arg_pos)
-    case default
-        print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
-                 "accepted modes and rerun."
-
-        stop 3
-         
-    end select
-end subroutine call_mode

src/call_option.f90

@@ -1,53 +0,0 @@
-subroutine call_option(option, arg_pos)
-    use parameters
-    use opt_disl
-    use opt_group
-    use opt_orient
-    use opt_deform
-    use opt_delete
-    use opt_redef_box
-    use opt_slip_plane
-    use box
-    implicit none
-
-    integer, intent(inout) :: arg_pos
-    character(len=100), intent(in) :: option
-
-    select case(trim(adjustl(option)))
-    case('-disl','-dislgen', '-disloop','-vacancydisloop')
-        call dislocation(option, arg_pos)
-    case('-group')
-        call group(arg_pos)
-    case('-ow')
-        arg_pos = arg_pos + 1
-    case('-wrap')
-        arg_pos = arg_pos + 1
-    case('-orient')
-        call orient(arg_pos)
-    case('-unorient')
-        call unorient
-        arg_pos = arg_pos + 1
-    case('-boundary')
-        arg_pos=arg_pos+1
-        call get_command_argument(arg_pos, box_bc)
-        arg_pos=arg_pos+1
-        bound_called = .true.
-    case('-sbox_ori')
-        call sbox_ori(arg_pos)
-    case('-deform')
-        call deform(arg_pos)
-    case('-delete')
-        call run_delete(arg_pos)
-    case('-set_cac')
-        arg_pos=arg_pos +3
-    case('-set_types')
-        arg_pos = arg_pos + 2 + atom_types
-    case('-redef_box')
-        call redef_box(arg_pos)
-    case('-slip_plane')
-        call run_slip_plane(arg_pos)
-    case default
-        print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
-        stop 3 
-    end select
-end subroutine call_option

src/caller.f90

@@ -0,0 +1,91 @@
+module caller
+    !this module just calls modes and options
+
+    use mode_create
+    use mode_convert
+    use mode_merge
+    use mode_metric
+    use mode_calc
+    use parameters
+    use opt_disl
+    use opt_group
+    use opt_orient
+    use opt_deform
+    use opt_delete
+    use opt_redef_box
+    use opt_slip_plane
+    use box
+
+
+    implicit none
+    public 
+    contains
+    subroutine call_mode(arg_pos)
+        !This code is used to parse the command line argument for the mode information and calls the required 
+        !mode module.
+    
+        integer, intent(out) :: arg_pos
+    
+        select case(mode)
+        case('--create')
+            call create(arg_pos)
+        case('--convert')
+            call convert(arg_pos)  
+        case('--merge')
+            call merge(arg_pos) 
+        case('--metric')
+            call metric(arg_pos)
+        case('--calc')
+            call calc(arg_pos)
+        case default
+            print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
+                     "accepted modes and rerun."
+    
+            stop 3
+        end select
+    end subroutine call_mode
+
+    subroutine call_option(option, arg_pos)
+        integer, intent(inout) :: arg_pos
+        character(len=100), intent(in) :: option
+    
+        select case(trim(adjustl(option)))
+        case('-disl','-dislgen', '-disloop','-vacancydisloop')
+            call dislocation(option, arg_pos)
+        case('-group')
+            call group(arg_pos)
+        case('-ow')
+            arg_pos = arg_pos + 1
+        case('-wrap')
+            arg_pos = arg_pos + 1
+        case('-orient')
+            call orient_opt(arg_pos)
+        case('-unorient')
+            call unorient
+            arg_pos = arg_pos + 1
+        case('-boundary')
+            arg_pos=arg_pos+1
+            call get_command_argument(arg_pos, box_bc)
+            arg_pos=arg_pos+1
+            bound_called = .true.
+        case('-sbox_ori')
+            call sbox_ori(arg_pos)
+        case('-deform')
+            call deform(arg_pos)
+        case('-delete')
+            call run_delete(arg_pos)
+        case('-set_cac')
+            arg_pos=arg_pos +3
+        case('-set_types')
+            arg_pos = arg_pos + 3 + atom_types
+        case('-redef_box')
+            call redef_box(arg_pos)
+        case('-slip_plane')
+            call run_slip_plane(arg_pos)
+        case default
+            print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
+            stop 3 
+        end select
+    end subroutine call_option
+
+end module caller

src/main.f90

@@ -15,6 +15,7 @@ program main
     use parameters
     use elements
     use io
+    use caller
     
  
     integer ::  i, end_mode_arg, arg_num, arg_pos

src/opt_orient.f90

@@ -16,7 +16,7 @@ module opt_orient
     public 
     contains
 
-    subroutine orient(arg_pos)
+    subroutine orient_opt(arg_pos)
 
         integer, intent(inout) :: arg_pos
 
@@ -82,7 +82,7 @@ module opt_orient
         end do
 
             call def_new_box
-    end subroutine orient
+    end subroutine orient_opt
 
     subroutine parse_orient(arg_pos)
         !This parses the orient option