The only way to initialise external memory attached to an FPGA is to write to it - via your configured FPGA.
Whilst you can initialise memory blocks
internal to the FPGA using it's configuration bitstream, you cannot initialise
external memory in the same way.
There are plenty of ways to write to (and read from) external SDRAM devices (including DDR3 memory). They all require the FPGA to be configured with an appropriate design capable of controlling the device(s). I suggest a Nios processor with the appropriate ALTMEMPHY peripheral connected might be the most appropriate way forward to allow you to 'initialise' the contents of your DDR3 memory.
Regards,
Alex