Added some calc and metric changes

src/Makefile

@@ -1,14 +1,15 @@
-FC=ifort
+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 -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 -O3 -g
 #FFLAGS=-mcmodel=large -O0 -g -fbacktrace -fcheck=all
 
-MODES=mode_create.o mode_merge.o mode_convert.o mode_metric.o
+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
 
@@ -23,7 +24,7 @@ cacmb: $(OBJECTS)
 
 .PHONY: clean
 clean: 
-	$(RM) cacmb  *.o *.mod
+	$(RM) cacmb  *.o *.mod *genmod*
 
 testfuncs: testfuncs.o functions.o subroutines.o
 	$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@

src/io.f90

@@ -600,7 +600,7 @@ module io
                 stop 3
             end if
             select case(trim(adjustl(mode)))
-            case('--convert','--metric')
+            case('--calc', '--convert','--metric')
                 infilenum = infilenum+1
                 infiles(infilenum) = temp_infile
             case default

src/main.f90

@@ -112,7 +112,7 @@ program main
 
     !Check to make sure a file was passed to be written out and then write out 
     ! Before building do a check on the file
-    if (trim(adjustl(mode)) /= "--metric") then    
+    if ((trim(adjustl(mode)) /= "--metric").and.(trim(adjustl(mode)) /= "--calc"))then    
         if ((outfilenum == 0)) then
             argument = 'none'
             call get_out_file(argument)

src/mode_metric.f90

@@ -93,10 +93,10 @@ module mode_metric
         call get_command_argument(2,metric_type,arglen)
         if (arglen == 0) stop "Incomplete mode metric command, check documentation"
         select case(trim(adjustl(metric_type))) 
-        case("microrotation")
+        case("microrotation", "def_grad")
             continue
         case default
-            print *, "Mode metric does not accept metric ", metric_type, ". Please select from: microrotation"
+            print *, "Mode metric does not accept metric ", metric_type, ". Please select from: microrotation, def_grad"
             stop 3
         end select
 
@@ -155,6 +155,7 @@ module mode_metric
                     do i = 1,3
                         do j = 1, 3
                             met(k, ip) = def_grad(i,j)   
+                            k = k + 1
                         end do
                     end do
                 case('microrotation')
@@ -228,7 +229,7 @@ module mode_metric
 
         if(atom_num > 0) then 
             do i = 1, atom_num
-                write(11,*) type_atom(i), r_atom(:,i), met(:,tag_atom(i))
+                write(11,*) 0, type_atom(i), r_atom(:,i), met(:,tag_atom(i))
             end do
         end if
 
@@ -236,7 +237,7 @@ module mode_metric
             do i = 1, ele_num
                 do inod = 1, ng_node(lat_ele(i))
                     do ibasis = 1, basisnum(lat_ele(i))
-                        write(11,*) basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i), &
+                        write(11,*) 1, basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i), &
                                     met(:, atom_num+(tag_ele(i)-1)*max_ng_node*max_basisnum + (inod-1)*max_basisnum + ibasis) 
                     end do
                 end do