Hibernate Arduino for 12hrs with rtc1302 module
You need 3 pieces of code and one replacement:

1) Ditch ds1302 and get yourself an RTC with an interrupt pin (like DS3231 which Jot suggests). It will make your life easier.

2) Setup your RTC to fire an interrupt every 12 hours.

3) Since you have successfully implemented a sleep mode, try to wake your Arduino up using a hardware interrupt. See Nick Gammon's guide for interrupts, and read carefully about waking your micro with an external interrupt. You can prototype it using a pushbutton, which will either connect your interrupt pin to GND or Vcc. Use an appropriate resistor as well. This guide has good information for starters.

To sum up: you'll have your Arduino sleep at all times and your RTC set to fire a hardware interrupt. When fired, the interrupt wakes Arduino, and the interrupt code will handle your measurements.