Working commit for dislocation generation branch

src/Makefile

@@ -1,8 +1,9 @@
 FC=ifort
 #FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
-FFLAGS=-mcmodel=large -Ofast
+FFLAGS=-mcmodel=large -Ofast -no-wrap-margin
 MODES=mode_create.o mode_merge.o mode_convert.o
-OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES)
+OPTIONS=opt_disl.o
+OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o call_option.o $(MODES) $(OPTIONS)
 
 .SUFFIXES:
 .SUFFIXES: .c .f .f90 .F90 .o
@@ -25,9 +26,10 @@ cleantest:
 	$(RM) testfuncs testfuncs.o
 
 $(OBJECTS) : parameters.o
-atoms.o subroutines.o testfuncs.o : functions.o
-main.o io.o build_subroutines.o: elements.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)
 $(MODES) io.o: atoms.o box.o
 $(MODES) main.o : io.o
-testfuncs.o elements.o mode_create.o: subroutines.o
+testfuncs.o elements.o mode_create.o opt_disl.o: subroutines.o

src/box.f90

@@ -1,7 +1,7 @@
 module box
     !This module contains information on the properties of the current box.
     use parameters
-
+    use functions
     implicit none 
 
     real(kind=dp) :: box_bd(6) !Global box boundaries
@@ -34,8 +34,14 @@ module box
 
         integer, intent(in) :: n
 
-        allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
+        integer :: i
 
+        allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
+        do i = 1, n
+            sub_box_ori(:,:,i) = identity_mat(3)
+            sub_box_bd(:,i) = 0.0_dp
+            sub_box_array_bd(:,:,i) = 1
+        end do
     end subroutine alloc_sub_box
 
     subroutine grow_sub_box(n)
@@ -58,7 +64,7 @@ module box
         call move_alloc(temp_bd, sub_box_bd)
 
         temp_array_bd(:,:,1:sub_box_num) = sub_box_array_bd
-        temp_array_bd(:,:,sub_box_num+1:) = 0.0_dp
+        temp_array_bd(:,:,sub_box_num+1:) = 1
         call move_alloc(temp_array_bd, sub_box_array_bd)
 
         return

src/functions.f90

@@ -232,4 +232,14 @@ END FUNCTION StrDnCase
         end if
     return
     end function is_equal
+
+    pure function unitvec(n,vec)
+        integer, intent(in) :: n
+        real(kind=dp), intent(in) :: vec(n)
+        real(kind=dp) :: unitvec(n)
+
+        unitvec = vec/norm2(vec)
+        return
+    end function unitvec
+
 end module functions

src/io.f90

@@ -409,7 +409,7 @@ module io
         end do
 
         !Write the number of atom types in the current model and all of their names
-        write(11,*) atom_types, (type_to_name(i), i=1, atom_types)
+        write(11,*) atom_types, (type_to_name(i)//' ', i=1, atom_types)
         !Write the number of lattice_types, basisnum and number of nodes for each lattice type
         write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
         !Now for every lattice type write the basis atom types
@@ -544,10 +544,14 @@ module io
             read(11,*) sub_box_bd(:,sub_box_num+i)
             sub_box_bd(:,sub_box_num+i) = sub_box_bd(:, sub_box_num+i) + displace(:)
             !Read in sub_box_array_bd
-            read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
-
+            read(11,*) ((sub_box_array_bd(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
         end do
-            sub_box_num = sub_box_num + n
+
+        !Add the existing element boundaries
+        sub_box_array_bd(:,1,sub_box_num+1:) = sub_box_array_bd(:,1,sub_box_num+1:) + atom_num
+        sub_box_array_bd(:,2,sub_box_num+1:) = sub_box_array_bd(:,2,sub_box_num+1:) + ele_num
+
+        sub_box_num = sub_box_num + n
 
         !Read in the number of atom types and all their names
         read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)

src/main.f90

@@ -17,7 +17,7 @@ program main
     use io
     
 
-    integer ::  i, end_mode_arg, arg_num
+    integer ::  i, end_mode_arg, arg_num, arg_pos
     character(len=100) ::  argument
 
     !Call initialization functions
@@ -37,12 +37,25 @@ program main
     end if
 
     !Now we loop through all of the arguments and check for passed options or for a filename to be written out
-    do i = end_mode_arg-1, arg_num
-        call get_command_argument(i, argument)
+    arg_pos = end_mode_arg
+    do while(.true.)
+        !Exit the loop if we are done reading
+        if(arg_pos > arg_num) exit
+
+        call get_command_argument(arg_pos, argument)
 
         !Check to see if a filename was passed
         if(scan(argument,'.',.true.) > 0) then 
             call get_out_file(argument)
+            arg_pos = arg_pos + 1
+
+        !Check to see if an option has been passed
+        else if(argument(1:1) == '-') then 
+            call call_option(argument, arg_pos)
+        !Otherwise print that the argument is not accepted and move on
+        else
+            print *, trim(adjustl(argument)), " is not accepted. Skipping to next argument"
+            arg_pos = arg_pos + 1
         end if
     end do
 

src/mode_create.f90

@@ -230,10 +230,10 @@ module mode_create
 
             case default
                 !If it isn't an option then you have to exit
+                arg_pos = arg_pos -1
                 exit
             end select
         end do
-
         !Calculate the lattice periodicity length in lattice units
         do i = 1, 3
             lattice_space(i) = norm2(orient(i,:))

src/parameters.f90

@@ -2,7 +2,12 @@ module parameters
 
     implicit none
 
+    !Default precision
     integer, parameter :: dp= selected_real_kind(15,307)
+    !Parameters for floating point tolerance
     real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
                                 lim_large = huge(1.0_dp)
+    !Numeric constants
+    real(kind=dp), parameter :: pi = 3.14159265358979323846_dp
+
 end module parameters

src/subroutines.f90

@@ -1,6 +1,7 @@
 module subroutines
     use parameters
     use functions
+    use box
     implicit none
 
     integer :: allostat, deallostat
@@ -170,4 +171,36 @@ module subroutines
         return
     end subroutine parse_ori_vec
 
+    subroutine parse_pos(i, pos_string, pos)
+        !This subroutine parses the pos command allowing for command which include inf
+        integer, intent(in) ::  i !The dimension of the position
+        character(len=100), intent(in) :: pos_string !The position string
+        real(kind=dp), intent(out) :: pos !The output parsed position value
+
+        integer :: iospara
+        if(trim(adjustl(pos_string)) == 'inf') then 
+            pos=box_bd(2*i)
+        else if(trim(adjustl(pos_string)) == '-inf') then
+            pos=box_bd(2*i-1)
+        else if ((index(pos_string,'-') > 0).and.(index(pos_string,'inf')>0)) then 
+            !Now extract the number we are reducing from infinity
+            read(pos_string(index(pos_string,'-')+1:), *, iostat=iospara) pos
+            pos = box_bd(2*i) - pos
+        else if ((index(pos_string,'+') > 0).and.(index(pos_string,'inf')>0)) then 
+            !Now extract the number we are reducing from infinity
+            read(pos_string(index(pos_string,'+')+1:), *, iostat=iospara) pos
+            pos = box_bd(2*i-1) + pos
+        else if ((index(pos_string,'*') > 0).and.(index(pos_string,'inf')>0)) then 
+            !Now extract the number we are reducing from infinity
+            read(pos_string(index(pos_string,'*')+1:), *, iostat=iospara) pos
+            pos = (box_bd(2*i)-box_bd(2*i-1))*pos
+        else
+            read(pos_string, *, iostat=iospara) pos
+        end if
+
+        if (iospara > 0) then 
+            print *, "Error reading position argument ", trim(adjustl(pos_string)), ". Please reformat and try again."
+        end if
+    end subroutine parse_pos
+
 end module subroutines