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Re: Constraint violated by particle
From: |
Ahmad Reza Motezakker |
Subject: |
Re: Constraint violated by particle |
Date: |
Wed, 28 Oct 2020 20:12:16 +0000 |
Dear Kai,
Thank you very much for the help. It worked.
Best Regards,
Ahmad Reza
Sent from my iPhone
> On 28 Oct 2020, at 15:03, Kai Szuttor <kai@icp.uni-stuttgart.de> wrote:
>
> Hi Ahmad,
>
> as I have mentioned changing the direction of the normal vectors fixes the
> issue.
> What you maybe did not do is also changing the sign of the distance. The idea
> is that
> the product of normal vector *and* distance gives a point on the wall
> surface. Therefor,
> to have a wall at z = 50 parallel to the x-y plane you would have to use
> normal=[0,0,-1]
> and dist=-50.
>
> Best,
>
> Kai
>
>> On Wed, Oct 28, 2020 at 09:32:20AM +0000, Ahmad Reza Motezakker wrote:
>> Dear Kai,
>>
>> Attached please find the minimal version. Thank you again.
>>
>> Best Regards,
>>
>> Ahmad Reza
>>
>> ----------------------------------------------------------------------
>>
>> From: Kai Szuttor <kai@icp.uni-stuttgart.de>
>> Sent: Wednesday, October 28, 2020 10:17 AM
>> To: Ahmad Reza Motezakker
>> Cc: espressomd-users@nongnu.org List
>> Subject: Re: Constraint violated by particle
>>
>> please attach a minimal not working example reproducing your issue
>>
>> Am 28.10.2020 um 09:50 schrieb Ahmad Reza Motezakker <armot@kth.se>:
>>
>>
>>
>> Dear Kai,
>>
>> Before sending my email, I tried to change the directions of the normal
>> vectors but it gave me the same error. To clarify it, Attached please
>> find the schematic of the way that i have defined the constraints and LB
>> boundaries and their normal vectors.
>>
>> Thank you very much.
>>
>> Best Regards,
>>
>> Ahmad Reza
>>
>> ----------------------------------------------------------------------
>>
>> From: Kai Szuttor <kai@icp.uni-stuttgart.de>
>> Sent: Wednesday, October 28, 2020 9:28 AM
>> To: Ahmad Reza Motezakker
>> Cc: espressomd-users@nongnu.org List
>> Subject: Re: Constraint violated by particle
>>
>> Hi Ahmad,
>> i guess your normal vectors are pointing in the wrong direction?
>> Best,
>> Kai
>>
>> Am 28.10.2020 um 09:23 schrieb Ahmad Reza Motezakker <armot@kth.se>:
>>
>>
>>
>> Dear All,
>>
>> I have a system of a polymer chain, LB fluid and wall constraints (a
>> small chain of polymer, Two wall for fluid boundary and at the same
>> place two wall constraints for setting up the wall-particle
>> interaction). I make the system in the order of creating the polymer
>> chain, fluid and its LB boundaries (Wall), and constraints. I do not
>> face any error during polymer warming up, equilibration, and
>> fluid-polymer warming up. I define the polymer far from the
>> constraints and add lennard-jones repulsion between the polymer and
>> constraints to avoid any constraint violation. I define the LB
>> boundaries and constraints as follows:
>>
>> -----------------------------------------------------
>>
>> logging.info("Setup LB boundaries.")
>> top_wall =
>>
>> espressomd.lbboundaries.LBBoundary(shape=espressomd.shapes.Wall(normal=[0,
>> 0, -1], dist=0))
>> bottom_wall =
>>
>> espressomd.lbboundaries.LBBoundary(shape=espressomd.shapes.Wall(normal=[0,
>> 0, 1], dist=50))
>> system.lbboundaries.add(top_wall)
>> system.lbboundaries.add(bottom_wall)
>> #for constraints only
>> TopWall = Wall(dist=0, normal = (0,0,-1))
>> BottomWall = Wall(dist = 50, normal=(0,0,1))
>> system.constraints.add(shape = TopWall, particle_type = 10,
>> penetrable=False)
>> system.constraints.add(shape = BottomWall, particle_type = 10,
>> penetrable=False)
>> -----------------------------------------------------
>> But when I run the integration, in the very very first step (while the
>> polymer is the middle of the box and far from the walls) I face the
>> error : Constraint violated by particle.
>> Could you please give me some hints on that? I really appreciate your
>> help.
>> Best Regards,
>> Ahmad Reza
>>
>> <boundaries.pdf>
>
>