Extracting Kappa

Hi all,

in the examples/KAPPA/README file it is written that:

Here is how to extract Kappa from the log file output for each method.

The NEMD methods use the formula kappa = dQ * dZ/dTemp where dQ =

energy flux, and dTemp/dZ = temperature gradient.

(1) in.langevin

dQ = 8000 * 0.5*(0.905+0.947) / 100 / 18.82^2 / 2

8000 atoms

0.5*(0.905+0.947) = from log file =

ave of total in/out energy for 2 regions normalized by # of atoms

100 = 20,000 steps at 0.005 tau timestep = run time in tau

xy box area = 18.82^2

divide by 2 since energy flux goes in 2 directions due to periodic z

dTemp = 0.578 from log file for average Temp difference between 2 regions

dZ = 18.82

Kappa = 3.41

I cannot understand why should we multiply by 8000 since f_hot and f_cold provide us with the cumulative energy added/subtracted to the atoms as they are thermostatted. Moreover, I cannot see a line in the input script (or in the log file) where averaging of the total in/out energy for 2 regions normalized by # of atoms is performed.

Many thanks for your help in advance.

Kind regards,


fhot and fcold as they appear in the log file (output of thermo command)

are normalized by the number of atoms, which is the default

for all thermo output in LJ units. So to get total energy

flux its multiplied by N = 8000 atoms then divided by

cross-section area. The area is effectively a normalization

by the size of the system.