diff --git a/src/initialize.F90 b/src/initialize.F90
index c37bc63381..06da79afb1 100644
--- a/src/initialize.F90
+++ b/src/initialize.F90
@@ -217,10 +217,10 @@ contains
 
   subroutine read_command_line()
 
-    integer :: i         ! loop index
-    integer :: argc      ! number of command line arguments
+    integer :: i ! loop index
+    integer :: argc ! number of command line arguments
     integer :: last_flag ! index of last flag
-    character(MAX_FILE_LEN) :: pwd      ! present working directory
+    character(MAX_FILE_LEN) :: pwd ! present working directory
     character(MAX_WORD_LEN), allocatable :: argv(:) ! command line arguments
     
     ! Get working directory
@@ -241,7 +241,7 @@ contains
     do while (i <= argc)
        ! Check for flags
        if (starts_with(argv(i), "-")) then
-          select case (argv(i))
+         select case (argv(i))
           case ('-p', '-plot', '--plot')
              plotting = .true.
           case ('-?', '-help', '--help')
@@ -250,7 +250,8 @@ contains
           case ('-v', '-version', '--version')
              call print_version()
              stop
-          case ('-eps_tol', '-ksp_gmres_restart')
+          case ('-eps_tol', '-ksp_gmres_restart','-eps_monitor','-eps_type',   &
+         &      '-snes_monitor','-ksp_monitor')
              ! Handle options that would be based to PETSC
              i = i + 1
           case default
@@ -261,33 +262,30 @@ contains
           last_flag = i
        end if
 
-      ! Determine directory where XML input files are
-      if (i == argc .and. last_flag /= i) then
-         last_flag = last_flag + 1
-         path_input = argv(last_flag)
-         ! Need to add working directory if the given path is a relative path
-         if (.not. starts_with(path_input, "/")) then
-            path_input = trim(pwd) // "/" // trim(path_input)
-         end if
-      else
-         last_flag = last_flag + 1
-         path_input = pwd
-      end if
        ! Increment counter
        i = i + 1
     end do
 
-    if (last_flag == 0) path_input = pwd
+    ! Determine directory where XML input files are
+    if (argc > 0 .and. last_flag < argc) then
+      path_input = argv(last_flag + 1)
+       ! Need to add working directory if the given path is a relative path
+       if (.not. starts_with(path_input, "/")) then
+         path_input = trim(pwd) // "/" // trim(path_input)
+       end if
+     else
+      path_input = pwd
+    end if
 
     ! Add slash at end of directory if it isn't there
     if (.not. ends_with(path_input, "/")) then
-       path_input = trim(path_input) // "/"
+      path_input = trim(path_input) // "/"
     end if
 
     ! Free memory from argv
     deallocate(argv)
 
-    ! TODO: Check that directory exists
+    ! TODO: Check that directory exists 
 
   end subroutine read_command_line