Re: calculating box length in charged system part2

[Jean-Noël Grad]

Dear Ahmad,

Looking at an earlier version of part 1, it looks like part 2 gives the 
density in u/A^3, with "A" for Angstroms and u the molecular mass ("u" 
is another symbol for Dalton; "u" is more common in physics while "Da" 
is more common in biophysics).

Since the variable "masses" stores molecular masses, the units check 
out. The choice of variable name is unfortunate. Nowadays, this kind of 
ambiguity can be avoided by using the python module `pint`, where all 
quantities have a unit, unfortunately it did not exist yet when this 
tutorial was written, and the tutorial was never updated.

Furthermore, the tutorial seems to give the wrong value for the density. 
I just double checked the referenced paper, where the formula at page 73 
is `d(T) = 2.1389 - 5.426e-4 * T`, which yields d=1.48870 at the 
temperature of the tutorial T=1198.3, instead of d=1.1138. Starting from 
the tutorial density, one can work out a temperature T=1889.3, so it's 
likely that the density is wrong due to a typo when 1198.3 was typed in.

In the future, this part of the tutorial will be removed and replaced by 
an ELC simulation 
(https://github.com/espressomd/espresso/issues/3955#issuecomment-712711556).

Best,
JN

On 11/6/20 7:57 PM, Ahmad Reza Motezakker wrote:
> Dear All,
>
>
> I was going through the tutorial for the charged system Part 2 and I did not 
> understand why in calculation of box length in x and y direction, we take into 
> account all the masses including electrode mass as follows:
>
> (box_l = (n_ionpairs * sum(masses.values()) / density)**(1. / 3.))
>
> which masses is : masses      = {"Cl":  35.453, "Na": 22.99, "Electrode": 12.01}
>
> ?I really appreciate your help
>
>
> Best Regards,
>
> Ahmad Reza