Re: [ESPResSo-users] Contents of Espressomd-users Digest, Vol 24, Issue 3, question 2

[Heng ZHANG]

Hi,

I found the contraints command for the use of tunable slip boundary interations 
for microchannel flows like Couette Flow, but I am not sure whether this is the 
shearing protocol I want. The parameters of types is not quite clear to me. 

Originally, I would like to shear the system by SLLOD algorithm, by moving the 
periodic boxes on the upper and lower row, generating the shear flow, which 
means the simulation boxes will be responsable for the action, while the NEMD 
codes here seems to be the plug flow. 

Looking forward to your insights, and have a nice weekend.

yours,
Heng Zhang 

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Today's Topics:

   1. Re: why does Espresso calculate interactions between neutral
      particles in debye huckel? (Olaf Lenz)
   2. Re: Shearing protocols in ESPResSo (Olaf Lenz)
   3. Re: why does Espresso calculate interactions between neutral
      particles in debye huckel? (Owen Hickey)


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Message: 1
Date: Fri, 19 Oct 2012 15:23:41 +0200
From: Olaf Lenz <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] why does Espresso calculate interactions
        between neutral particles in debye huckel?
Message-ID: <address@hidden>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hi!

On 10/18/2012 04:13 PM, amir khosravani wrote:
> I have many simulations that these simulations have neutral and
> charged particles, and the number of neutral particles are more than
> charged particles. I used debye huckel interaction; and my programs
> are very slow. I have tested and understood that Espreeso calculates
> the interactions between neutral particles and charged-neutral
> particles, whereas these interactions are zero. Are you have any idea
> about the solution of this problem?

I do not completely understand your mailing. You have charged and
neutral particles. The charged particles interact via the Debye-Hueckel
potential, to model the Coulomb interaction. However, the neutral
particles so also interact via some kind of LJ potential or the like,
don't they? Therefore, they also take some time. If the neutral
particles would not interact at all, why would you include them into the
simulation in the first place?

Olaf

--
Dr. rer. nat. Olaf Lenz
Institut f?r Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
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Message: 2
Date: Fri, 19 Oct 2012 15:31:05 +0200
From: Olaf Lenz <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] Shearing protocols in ESPResSo
Message-ID: <address@hidden>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hi!

On 10/18/2012 03:13 PM, Heng ZHANG wrote:
> I am trying to add shear to my polymer system with Couette flow, but
> so far I only found the codes in ESPResSo of RNEMD methods. I am
> wondering whether there are codes about Couette flow?

ESPResSo does not contain any other method for shearing than NEMD at the
moment. Implementing another method should not be very hard, however.

Wouldn't NEMD create a Couette flow? Or what kind of other shearing
protocol are you thinking of?

Olaf

--
Dr. rer. nat. Olaf Lenz
Institut f?r Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
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Message: 3
Date: Fri, 19 Oct 2012 15:47:49 +0200
From: Owen Hickey <address@hidden>
To: address@hidden
Cc: address@hidden
Subject: Re: [ESPResSo-users] why does Espresso calculate interactions
        between neutral particles in debye huckel?
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset="iso-8859-1"

Hey,

I think his point is that there is a surprising large slowdown of the
simulations when he turns on the Debye-Hueckel interaction even though he
has relatively few charged particles.  It is true the underlying code
calculates the DH interaction between all particles within the cutoff.  You
could try adding an if (p1->q*p2->q!=0) before the call is made but you
might still find it much slower.  This is because that even for the short
ranged interactions between neutral particles the cutoff for the DH
interaction would be used as their is only one neighbor list in Espresso.

I would recommend first trying to use P3M as there is a good chance it
provides acceptable performance.  Adding an if to the c code might also
help though I suspect that it might still be slower than switching to P3M.

Owen

On Fri, Oct 19, 2012 at 3:23 PM, Olaf Lenz <address@hidden>wrote:

> Hi!
>
>
> On 10/18/2012 04:13 PM, amir khosravani wrote:
>
>> I have many simulations that these simulations have neutral and
>> charged particles, and the number of neutral particles are more than
>> charged particles. I used debye huckel interaction; and my programs
>> are very slow. I have tested and understood that Espreeso calculates
>> the interactions between neutral particles and charged-neutral
>> particles, whereas these interactions are zero. Are you have any idea
>> about the solution of this problem?
>>
>
> I do not completely understand your mailing. You have charged and
> neutral particles. The charged particles interact via the Debye-Hueckel
> potential, to model the Coulomb interaction. However, the neutral
> particles so also interact via some kind of LJ potential or the like,
> don't they? Therefore, they also take some time. If the neutral
> particles would not interact at all, why would you include them into the
> simulation in the first place?
>
> Olaf
>
> --
> Dr. rer. nat. Olaf Lenz
> Institut f?r Computerphysik, Allmandring 3, D-70569 Stuttgart
> Phone: +49-711-685-63607
>
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