Re: [ESPResSo-users] Object in Fluid

[Wink, Markus]

Dear Ivan,

thank you very much for your answer. Your tutorial helped me a lot! Thanks. 
 
I ran the simulation on one core for a box with the dimension 22x50x27, agrid = 
1 and a = 0.001. It works fine, the particle reaches the obstacle and passes 
it. 

Greetings 

Markus


-----Ursprüngliche Nachricht-----
Von: Ivan Cimrak [mailto:address@hidden 
Gesendet: Donnerstag, 24. Juli 2014 10:33
An: Wink, Markus
Cc: Andrew Jewett; address@hidden
Betreff: Re: AW: AW: AW: [ESPResSo-users] Object in Fluid

Dear Markus,

1. Now, I am not sure whether the setting agrid=1.0 solves your problem with 
the big simulation on one core. Does your simulation with box 22x50x27, agrid = 
1 and a = 0.001 works fine?

2. When computing in parallel, you need to be sure that the splitting of your 
big domain generates local boxes of dimension compatible with agrid. Imagine 
you have large box 10x10x10 and you want to use 16 cores. 
One possible splitting is to divide x direction into two parts, y direction 
into 2 parts and z direction into 4 parts. This will divide large domain into  
16 smaller parts. However, the dimension of smaller parts will be 5x5x2.5. And 
this is incompatible with agrid, since LB grid is one. Therefore in this 
particular case you may use 8 cores, which will divide large domain into 8 
parts with dimensions 5x5x5.

There are variables in Espresso like local_box, min_global_cut, skin, and these 
variables (in addition to some other things) determine, how the domain is 
eventually split when running parallel. I wrote a short tutorial on this topic, 
see the attachment. I do not guarantee that the tutorial is 100% correct, 
however, it helps us to set the right values.

I hope this helps,
Ivan

Dňa 24.7.2014 10:03 Wink, Markus wrote / napísal(a):
> 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
>


--
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