temperature of the fluide

Calculate cubic centimeters per Mole by dividing the atomic weight by the density in grams per cubic centimeter. Then you can divide Avogadro's number by the previously calculated number to get the number of atoms per cubic centimeter. Then you need to relate the fluence to the deposition rate, you can for instance multiply that number by 0.0000001 to convert it to nanometers per area per unit time and then multiply by your deposition rate in nm/s. You probably calibrate your deposition monitor with film measurements taken at room temperature so you shouldn't need to factor that in.

Example: Depositing Au @ 10nm/s

Au - Atomic Weight = 196.9665, Density @ 20C = 19.32

196.9665/19.32 = 10.19495 (this gives you cubic centimeters per Mole)

6.022E+23/10.19495 = 5.9068E+22 (this gives you the number of atoms per cc)

Because fluence is per unit area per unit time, you can now simply multiply the last result by the deposition rate in centimeters/unit time and you have your value for fluence. 

1nm = 0.0000001cm so 5.9068E+22 X 0.0000001 = 5.9068E+15 (atoms per nm in an area of 1cm square)

Multiply by deposition rate (per nm) 10 X 5.9068E+15 = 5.9068E+16

Fluence = 5.9068E+16 atoms per second per centimeter square.