Re: [ESPResSo-devel] A bug in Espresso

[Ivan Cimrak]

That could be the reason. Thanks very much for the explanation!

Just to be sure, you have shifted the lb lattice by a half grid point.
Does that mean that if I set the fluid velocity by
lbnode 0 0 0
that it is set in the spatial point 0.5 0.5 0.5? Or at -0.5 -0.5 -0.5?

Also, if I set a wall constraint by
constraint wall dist 0.5 normal 0 0 1
should I set the lbboundary shifted? Do I need to set
lbboundary wall dist 1.0 normal 0 0 1
or
lbboundary wall dist 0.0 normal 0 0 1
?

Thanks,
Ivan


On Fri, Jun 29, 2012 at 3:57 PM, Axel Arnold
<address@hidden> wrote:
> Hi!
>
> There was a small change in Espresso 3.0.2-> 3.1.0. In the older version,
> lattice grid points were located at integer positions, now they are shifted by
> half a grid spacing. This has big advantages with the parallelization, e.g.
> the "cellsystem domain_decomposition -no_verlet_list" no longer required.
> However, because of this, your imposed flow is now half a lattice spacing off
> compared to the old code.
>
> Unfortunately, we forgot to put that into the NEWS /CHANGES file.
>
> Axel
>
>
> On Friday 29 June 2012 15:25:03 Ulf Schiller wrote:
>> Hi Ivan,
>>
>> On 06/29/2012 01:37 PM, Ivan Cimrak wrote:
>> > Hello,
>> >
>> > I have been using Espresso quite some time. Together with Markus
>> > Gusenbauer from FH Sankt Poelten we have done some extensions. During
>> > my tests I found out that the version 3.0.2 does not compute the same
>> > results as the 3.1.0 does.
>> >
>> > I did the following test:
>> > 2 particles bonded with harmonic interaction. I put them in the
>> > lbfluid, I set the velocity of the fluid on the left side of the
>> > channel  and I look at the positions of both particles and their
>> > distance. I compiled two versions from your sources available at
>> > http://espressomd.org/wordpress/download/. In both cases I compiled
>> > only the LB and LB_BOUNDARIES in. With these two versions I obtained
>> > different results.
>> >
>> > I attach two output files.
>> >
>> > Do you have any idea why is it so?
>>
>> I had a quick look at your data and at first glance it seems there is
>> only a numerical difference. Do you think the results are physically
>> incorrect? The difference seems to be that the coupling between
>> particles and fluid sets in at different time steps (i=11 in 310.dat and
>> i=12 in 302.dat). This could be due to round-off differences in the two
>> versions of ESPResSo. The results should converge for dt->0.
>>
>> Hope this helps,
>> Ulf
>>
>> > TCL code:
>> > set vmd "n"
>> > setmd time_step 0.1;
>> > setmd skin 0.2;
>> > thermostat off;
>> >
>> > set pipeX 50; set pipeY 20; set pipeZ 20;
>> > setmd box_l $pipeX $pipeY $pipeZ;
>> >
>> > part 0 pos 10 10 10 type 1;
>> > part 1 pos 15 10 10 type 1;
>> > inter 0 harmonic 0.1 5.0;
>> > part 0 bond 0 1;
>> >
>> > cellsystem domain_decomposition -no_verlet_list
>> > lbfluid grid 1.0 dens 1.0 visc 1.0 tau 0.1 friction 1.0
>> >
>> > set upscale 5.;
>> > if { $vmd == "y" } { prepare_vmd_connection simEspresso 3000 1
>> > $upscale; exec sleep 1; imd positions $upscale; }
>> >
>> > set fp [open "output.dat" "w"]
>> > set i 0
>> > while { $i<  500 } {
>> >
>> >     puts "$i";
>> >
>> >      if { $vmd == "y"} { imd positions $upscale; }
>> >
>> >     for { set ii 0 } { $ii<  1} { incr ii } { for { set j 0 } { $j<
>> >
>> > $pipeY } { incr j } { for { set k 0 } { $k<  $pipeZ } { incr k } {
>> >
>> >                                     lbnode $ii $j $k set u 0.5 0.0 0.0;    
>> >  } } }
>> >
>> >     set aa [part 0 print pos]; set coraa [expr [lindex $aa 0]];
>> >     set bb [part 1 print pos]; set corbb [expr [lindex $bb 0]];
>> >
>> >     puts $fp "$i:   $coraa, $corbb, [expr $corbb - $coraa]";
>> >
>> >      integrate 1;
>> >      incr i
>> >
>> > }
>> > close $fp;
>> >
>> >
>> > -------------------------
>> > Dr. Ivan Cimrak
>> > Dep. Software Technologies, University of Zilina, Slovakia
>> > web: www.kst.fri.uniza.sk/~icimrak
> --
> JP Dr. Axel Arnold
> ICP, Universität Stuttgart
> Pfaffenwaldring 27
> 70569 Stuttgart, Germany
> Email: address@hidden
> Tel: +49 711 685 67609