Re: [ESPResSo-users] Object in Fluid

[Wink, Markus]

Dear Ivan,

I have checked the different configurations for a_grid (as you proposed in your 
last Email). If I change a_grid to 1, everything works just fine: the particle 
follows the stream lines of the fluid and passes the obstacle without any 
problems. But when I ran the original script I sent on July 15, I again get the 
error message (in both simulations the soft-sphere potential was chosen to have 
a factor a=0.001):
        broken: particles sum 2, id 0, partn 2, bond 2346
Afterwards, the no more integration steps are performed, although Espresso is 
still running (checked it using the top-command on the console). This I find 
very strange. The end configuration (when the error message occurs) you can 
find attached.

Another thing that bothers me concerns parallel computing using mpirun. I found 
out, that, depending on the box size I chose, it is possible, that Espresso 
escapes with the following error message:
        background_errors 0 {097 Lattice spacing agrid=1.000000 is incompatible 
with local_box_l[0]=5.500000 (box_l[0]=22.000000 node_grid[0]=4) 0.500000} 1 
<consent> 2 <consent> 3 <consent> 4 <consent> 5 <consent> 6 <consent> 7 
<consent> 8 <consent> 9    <consent> 10 <consent> 11 <consent> 12 <consent> 13 
<consent> 14 <consent> 15 <consent> 16 <consent> 17 <consent> 18 <consent> 19 
<consent> 20 <consent> 21 <consent> 22 <consent> 23 <consent> 24 <consent> 25 
<consent> 26 <consent> 27       <consent> 28 <consent> 29 <consent> 30 
<consent> 31 <consent>

The error message occurs with the following box size and the command "mpirun -n 
32" (my system provides 32 nodes I can run Espresso on):
        set width 20.
        set length 50.
        set height 27.
        # rectangular channel box geometry
        set boxX [expr $width+2]
        set boxY $length
        set boxZ [expr $height+2]
        setmd box_l $boxX $boxY $boxZ

If I run the simulation on only one node, I don't get that error message. So 
parallel computing discretizes the grid in some way (which I don't understand 
yet) and the a_grid (I chose agrid = 1) does not fit the node_grid. So I tried 
to have a look in the source code to find out, where "node_grid" is defined and 
to check, whether I can change it, but unfortunately I could not find it. 
Does anyone have a clue and can help me out?

Greetings

Markus

-----Ursprüngliche Nachricht-----
Von: Ivan Cimrak [mailto:address@hidden 
Gesendet: Mittwoch, 23. Juli 2014 13:30
An: Wink, Markus
Cc: Andrew Jewett; address@hidden
Betreff: Re: AW: AW: [ESPResSo-users] Object in Fluid

Dear Markus,

I have noticed that you use agrid 0.5. This might be a problem although we do 
not know why. All our tests were run with agrid = 1 and all worked fine. This 
issue is on our "to do" list.

Regarding your questions: once you change agrid to 1, the simulation runs 
perfect.
The big simulation, also, when I put agrid=1 to your first simulation, and I 
take a = 0.001 everything is perfect.

Can you check it?

What I find strange is that when I take your original code you sent on 15july, 
I change a to 0.001, then even with agrid=0.5 I don't get message with particle 
tearing apart. I attach the code.

Best,
Ivan


Dňa 22.7.2014 13:47 Wink, Markus wrote / napísal(a):
> Dear Ivan,
>
> thanks for your help and for the nice video! I tried your script (with the 
> configurations you chose, i. e. smaller channel for faster computation) and 
> it worked fine. But still, I have some problems which I have no idea how to 
> handle.
>
> 1) I tried a script with my geometry (which was bigger than yours) and 
> different parameters for a:  a = 1, a = 0.1, a = 0.01, a = 0.0005, a= 
> 0.00005, a= 0.000005. Still, I get the same error message, telling me, that 
> my particle tears apart. This is quite strange, since at least for the 
> configuration with the smallest a, the force acting on the particle by the 
> obstacle is in the order of magnitude of the fluidic force.
>
> So it seems, that the size of the object plays an important role for the 
> stability of the simulation. I don't really understand, where the problem 
> comes from, maybe you have an idea. And probably you also have an idea for my 
> first question, why still the particle tears apart when reaching the 
> obstacle, although I have changed the factor a to a very low value.
>
> Greetings and thanks a lot,
>
> Markus
>    
>
>
> Markus Wink
> _________________________________________________________
> Fraunhofer ICT-IMM
> Doktorand Abteilung Mikrofluidik und Analytik / Microfluidics and 
> Analytics Department Carl-Zeiss-Straße 18-20, 55129 Mainz, Germany 
> Phone +49 6131 990-396 / Fax +49 6131 990-205 
> address@hidden / www.imm.fraunhofer.de
>
>
> -----Ursprüngliche Nachricht-----
> Von: Ivan Cimrak [mailto:address@hidden
> Gesendet: Donnerstag, 17. Juli 2014 13:11
> An: Wink, Markus
> Cc: Andrew Jewett; address@hidden
> Betreff: Re: AW: [ESPResSo-users] Object in Fluid
>
> Dear Markus,
>
> I put the scripts in the attachment. I just ran the simulation once 
> again, and you can see the result on the video 
> https://www.dropbox.com/s/13gcp7ftielmo5i/sphere-passes-obstacle.avi
>
> soft_sphere was activated with parameters inter 0 10 soft-sphere 
> 0.0005 1.2 0.1 0.0
>
> Maybe, when you used too weak soft_sphere (your parameter was 10^(-6) whereas 
> mine was 10^(-4)), what happend was that the particles entered the boundary. 
> But in that case you would have gotten different error message.
>
> Markus, keep me please informed whether you can resolve this issue.
>
> Best,
> Ivan
>
>
>
>
> Dňa 17.7.2014 9:58 Wink, Markus wrote / napísal(a):
>> Dear Ivan,
>>
>> thanks for your advice. I have tried to lower the factor a as you proposed. 
>> I used a = 5*10^-6 , corresponding to a force of f = 9.5*10^-4.
>> But still, the particle tears apart. Strange.
>> If you still got the script, which you ran and which worked, would you be so 
>> kind to send it to me, so I can check, if I made another stupid mistake?
>>
>> Greetings and thanks a lot!
>>
>> Markus
>>
>>
>>
>> -----Ursprüngliche Nachricht-----
>> Von: Ivan Cimrak [mailto:address@hidden
>> Gesendet: Mittwoch, 16. Juli 2014 22:56
>> An: Wink, Markus
>> Cc: Andrew Jewett; address@hidden
>> Betreff: Re: [ESPResSo-users] Object in Fluid
>>
>> Dear Markus,
>>
>> The error message you have obtained indeed means that the bond of the object 
>> tears apart. The reason for this is that you have too strong soft_sphere 
>> potential. Your forces due to f_body are approximately 0.00156.
>>
>> On the other hand, soft_sphere potential is given by V(r)=a/(r^n), the 
>> forces due to soft_sphere are thus F(r)=dV/dr=a*n/(r^{n+1}).
>> Now your soft_sphere potential starts to act at the distance 0.1 from 
>> the obstacle (your cut-off was 0.1) but this means that the particles 
>> immediately get the force of
>> 1.0*1.2/(0.1^2.2) = 190.18  which is way too large. The system gets shock 
>> and then it blows apart.
>>
>> I would suggest to set soft_sphere much lower, say e.g. a = 0.0005 (or even 
>> smaller). This results to force 0.0005*1.2/(0.1^2.2)=0.095 which is 
>> acceptable. I have tried this setting with smaller channel (for faster 
>> computations) and it worked.
>>
>> Best regards,
>>
>> Ivan
>>
>> On Wed, Jul 16, 2014 at 8:28 AM, Wink, Markus <address@hidden> wrote:
>>> Dear all,
>>>
>>> attached you will find pictures of the starting configuration and the 
>>> configuration, when the simulation stops with the error message (actually 
>>> Espresso is not cancelled, but no further integration step will be 
>>> performed).
>>>
>>> Looking forward to your answers.
>>>
>>> Greetings
>>>
>>> Markus
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: Andrew Jewett [mailto:address@hidden
>>> Gesendet: Dienstag, 15. Juli 2014 17:59
>>> An: Wink, Markus
>>> Cc: address@hidden
>>> Betreff: Re: [ESPResSo-users] Object in Fluid
>>>
>>> Pictures can be helpful.
>>> What does the system look like (at nearby times)?
>>> Cheers
>>>
>>> Andrew
>>>
>>> On Tue, Jul 15, 2014 at 11:31 AM, Wink, Markus <address@hidden> wrote:
>>>> Dear all,
>>>>
>>>>
>>>>
>>>> I tried to simulate the movement of a particle past an obstacle 
>>>> inside a microfluidic channel using the oif method. At the moment I 
>>>> am facing the problem, that, when the particle gets near the 
>>>> object, the simulation stops and prints out the error message:
>>>>
>>>>
>>>>
>>>> “broken: particles sum 2, id 0, partn 2, bond 2346”
>>>>
>>>>
>>>>
>>>> I am not exactly sure, what that error message means. I guess, that 
>>>> the bond of the object tears apart, so I could change the parameters of 
>>>> the bond.
>>>> Does anyone have a clue? For the potential between the particle and 
>>>> the obstacle, I have chosen a soft sphere potential.
>>>>
>>>>
>>>>
>>>> The files are attached.
>>>>
>>>> Thanks a lot for your help.
>>>>
>>>>
>>>>
>>>> Greetings
>>>>
>>>>
>>>>
>>>> Markus
>>
>> --
>> Ivan Cimrak
>> FRI Zilinska Univerzita v Ziline
>> personal web: http://www.kst.fri.uniza.sk/~icimrak/
>> cell-in-fluid group: http://cell-in-fluid.fri.uniza.sk
>
> --
> Ivan Cimrak
> FRI Zilinska Univerzita v Ziline
> personal web: http://www.kst.fri.uniza.sk/~icimrak/
> cell-in-fluid group: http://cell-in-fluid.fri.uniza.sk
>


--
Ivan Cimrak
FRI Zilinska Univerzita v Ziline
personal web: http://www.kst.fri.uniza.sk/~icimrak/
cell-in-fluid group: http://cell-in-fluid.fri.uniza.sk

final configuration.png
Description: final configuration.png