From 86cdf3af95440f147a3e3513dab19ed192c29537 Mon Sep 17 00:00:00 2001
From: Paul Romano <romano7@gmail.com>
Date: Mon, 2 Apr 2012 14:11:37 -0400
Subject: [PATCH] Added check for command line flags used for PETSC.

---
 src/initialize.F90 | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/initialize.F90 b/src/initialize.F90
index 677e7ee969..c018efa3fc 100644
--- a/src/initialize.F90
+++ b/src/initialize.F90
@@ -221,19 +221,24 @@ contains
     integer :: argc      ! number of command line arguments
     integer :: last_flag ! index of last flag
     character(MAX_FILE_LEN) :: pwd      ! present working directory
-    character(MAX_WORD_LEN) :: argv(10) ! command line arguments
+    character(MAX_WORD_LEN), allocatable :: argv(:) ! command line arguments
     
     ! Get working directory
     call GET_ENVIRONMENT_VARIABLE("PWD", pwd)
 
-    ! Check number of command line arguments
+    ! Check number of command line arguments and allocate argv
     argc = COMMAND_ARGUMENT_COUNT()
 
-    ! Get all command line arguments
-    last_flag = 0
+    ! Allocate and retrieve command arguments
+    allocate(argv(argc))
     do i = 1, argc
        call GET_COMMAND_ARGUMENT(i, argv(i))
+    end do
 
+    ! Process command arguments
+    last_flag = 0
+    i = 1
+    do while (i <= argc)
        ! Check for flags
        if (starts_with(argv(i), "-")) then
           select case (argv(i))
@@ -245,6 +250,9 @@ contains
           case ('-v', '-version', '--version')
              call print_version()
              stop
+          case ('-eps_tol', '-ksp_gmres_restart')
+             ! Handle options that would be based to PETSC
+             i = i + 1
           case default
              message = "Unknown command line option: " // argv(i)
              call fatal_error()
@@ -252,6 +260,9 @@ contains
 
           last_flag = i
        end if
+
+       ! Increment counter
+       i = i + 1
     end do
 
     ! Determine directory where XML input files are
@@ -270,6 +281,9 @@ contains
        path_input = trim(path_input) // "/"
     end if
 
+    ! Free memory from argv
+    deallocate(argv)
+
     ! TODO: Check that directory exists
 
   end subroutine read_command_line