Re: calculating box length in charged system part2

[Ahmad Reza Motezakker]

Dera Jean-Noel,

Thank you very much for the help. 

Best Regards,
Ahmad Reza
________________________________________
From: Espressomd-users <espressomd-users-bounces+armot=kth.se@nongnu.org> on 
behalf of Jean-Noël Grad <jgrad@icp.uni-stuttgart.de>
Sent: Friday, November 6, 2020 10:16 PM
To: espressomd-users@nongnu.org
Subject: Re: calculating box length in charged system part2

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
>