Re: calculating MSD in tutorial LBM part3

[Ahmad Reza Motezakker]

Dear Jean-Noel,

Thank you very much.

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: Tuesday, November 17, 2020 8:29 PM
To: espressomd-users@nongnu.org
Subject: Re: calculating MSD in tutorial LBM part3

Dear Ahmad,

You can generate the HTML version of the 4.1.4 tutorials locally with
the command `make -j2 tutorials_html`, if you find it helpful. We use
that command to deploy the 4.2 tutorials to our website.

There is no release date for 4.2 yet. You can see our progress here:
https://github.com/espressomd/espresso/milestone/8

Best,
JN

On 11/17/20 6:27 PM, Ahmad Reza Motezakker wrote:
> Dear Jean-Noel,
>
> Thanks for the reply. When the 4.2 version will be released? because the 
> latest available version is 4.1.4 and it is returning N by 5 matrix.
>
> 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: Tuesday, November 17, 2020 5:56 PM
> To: espressomd-users@nongnu.org
> Subject: Re: calculating MSD in tutorial LBM part3
>
> Dear Ahmad,
>
> The MSD correlator has changed in 4.2. Calling method `.result()` now
> returns a N by 3 matrix, therefore the numpy sum applies to x,y,z
> triples and returns an array of length N.
>
> Regarding .lag_times(), you probably made a typo (it takes an extra
> "s"). If not, could you please share with us the error message when
> calling that method, and the git commit you're currently using?
>
> Best,
> JN
>
> On 11/17/20 5:18 PM, Ahmad Reza Motezakker wrote:
>> Dear All,
>>
>>
>> I was checking the third part of LBM tutorial 
>> (http://espressomd.org/html/tutorials_html/04-lattice_boltzmann/04-lattice_boltzmann_part3.html)
>>  and I noticed a point.
>>
>> As far as I know, The output of MSD correlator is in order of lag time, # of 
>> points, MSD_x, MSD_y, and MSD_z (am I right?)
>>
>> In calculating the MSD, according to the code, it is going to sum all the 
>> five columns (including lag time and the # o points) for each time step as 
>> follows:
>>
>> com_pos_msd_results.append(np.sum(com_pos_cor.result(), axis=1))
>>
>> That is how I understand, am I making a mistake?
>>
>> Moreover, the .lag_time() seems not working in the new versions.
>>
>> I really appreciate that if you let me know your opinion.
>>
>>
>> Best Regards,
>>
>> Ahmad Reza
>>
>