in /boot/config.txt

dtparam=i2c_arm=on

reboot

sudo apt-get install python-smbus i2c-tools

sudo i2cdetect -y 1

     0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f
00:          -- -- -- -- -- -- -- -- -- -- -- -- -- 
10: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
20: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
30: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
40: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
50: -- -- -- -- -- -- -- 57 -- -- -- -- -- -- -- -- 
60: -- -- -- -- -- -- -- -- 68 -- -- -- -- -- -- -- 
70: -- -- -- -- -- -- -- --  

to /boot/config.txt

dtoverlay=i2c-rtc,ds3231

reboot

sudo i2cdetect -y 1

     0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f
00:          -- -- -- -- -- -- -- -- -- -- -- -- -- 
10: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
20: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
30: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
40: -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 
50: -- -- -- -- -- -- -- 57 -- -- -- -- -- -- -- -- 
60: -- -- -- -- -- -- -- -- UU -- -- -- -- -- -- -- 
70: -- -- -- -- -- -- -- --  

sudo apt-get -y remove fake-hwclock &
sudo update-rc.d -f fake-hwclock remove &
sudo systemctl disable fake-hwclock

edit

sudo nano /lib/udev/hwclock-set

comment these lines:

(7,8, 9)

if [ -e /run/systemd/system ] ; then
 exit 0
fi

29:

/sbin/hwclock --rtc=$dev --systz --badyear

32:

/sbin/hwclock --rtc=$dev --systz

reboot

The folks that designed the DS3231 were very kind and made the temperature registers user-readable, so we can use it as a thermometer! How neat is that! The temperature is stored in registers 0x11 and 0x12 and is reported in 0.25ºC increments, though keep in mind the sensor is only accurate to ±3ºC. This forum post includes a sample python script that reads those registers and displays the output. It needs to be run with root privileges, and it will briefly unload the RTC kernel module in order to access the device, though this shouldn't matter given how quickly it runs.

lm-sensors includes a driver that can read the DS3231's temperature sensor. Install the lm-sensors package, then run 'sensors'.

ds3231-i2c-1-68
Adapter: bcm2835 (i2c@7e804000)
temp1:        +30.8°C

cpu_thermal-virtual-0
Adapter: Virtual device
temp1:        +48.9°C

cat /sys/class/i2c-dev/i2c-1/device/1-0068/hwmon/hwmon2/temp1_input

import smbus
import os

bus = smbus.SMBus(1)
address = 0x68

os.system('sudo rmmod rtc_ds1307')
def getTemp(address):
   byte_tmsb = bus.read_byte_data(address,0x11)
   byte_tlsb = bin(bus.read_byte_data(address,0x12))[2:].zfill(8)
   return byte_tmsb+int(byte_tlsb[0])*2**(-1)+int(byte_tlsb[1])*2**(-2)

#print getTemp(address)
Celsius = getTemp(address)
Fahrenheit = 9.0/5.0 * Celsius + 32
print Fahrenheit, "*F /", Celsius, "*C"
os.system('sudo modprobe rtc_ds1307')

Save as a .py file (e.g. ds3231_temp.py) and run with sudo python ds3231_temp.py

You may need to install python-smbus