Re: [ESPResSo-users] Correct usage of virtual sites

[Markus Gusenbauer]

Hi Christoph,

thanks for the hint, it worked right away with

"analyze set topo_part_sync"

Cheers,
Markus


On 16.05.2014 18:53, Christoph Junghans wrote:
> Hi Markus,
>
> 2014-05-16 7:50 GMT-06:00 Markus Gusenbauer <address@hidden>:
> > Dear users,
> >
> > has someone of you experience with the usage of virtual sites and especially
> > VIRTUAL_SITES_COM? I created a minimum tcl-script but it is not working. I
> > have a cube that is bonded with a simple FENE potential, right in the center
> > is a virtual site. After integration the virtual site position is NaN. Any
> > ideas what could be the problem?
> I think you need to call
> "analyze set topo_part_sync"
> after
> analyze set 0 "0 1 2 3 4 5 6 7 8"
>
> Otherwise try to compile with VIRTUAL_SITES_DEBUG on.
>
> Cheers,
>
> Christoph
> > Thanks,
> > Markus
> >
> > Here is the tcl:
> >
> > setmd time_step 0.1
> > setmd skin 0.2
> > thermostat off
> >
> > setmd box_l 20 20 20
> >
> > part 0 pos 10 10 10 mol 0
> > part 1 pos 12 10 10 mol 0
> > part 2 pos 12 10 12 mol 0
> > part 3 pos 10 10 12 mol 0
> > part 4 pos 10 12 10 mol 0
> > part 5 pos 12 12 10 mol 0
> > part 6 pos 12 12 12 mol 0
> > part 7 pos 10 12 12 mol 0
> > part 8 pos 11 11 11 virtual 1 mol 0
> >
> > inter 0 fene 10.0 0.1 2.0
> >
> > part 0 bond 0 1
> > part 1 bond 0 2
> > part 2 bond 0 3
> > part 3 bond 0 0
> > part 4 bond 0 5
> > part 5 bond 0 6
> > part 6 bond 0 7
> > part 7 bond 0 4
> > part 0 bond 0 4
> > part 1 bond 0 5
> > part 2 bond 0 6
> > part 3 bond 0 7
> >
> > analyze set 0 "0 1 2 3 4 5 6 7 8"
> >
> > set cycle 0
> > while { $cycle<10 } {
> >      puts "$cycle: vs pos=[part 8 print pos]"
> >      integrate 1
> >      incr cycle
> > }
> >
> > puts "\ncode_info: [code_info]"
> >
> >
> > And the output:
> >
> >
> > 0: vs pos=11.0 11.0 11.0
> > 1: vs pos=-NaN -NaN -NaN
> > 2: vs pos=-NaN -NaN -NaN
> > 3: vs pos=-NaN -NaN -NaN
> > 4: vs pos=-NaN -NaN -NaN
> > 5: vs pos=-NaN -NaN -NaN
> > 6: vs pos=-NaN -NaN -NaN
> > 7: vs pos=-NaN -NaN -NaN
> > 8: vs pos=-NaN -NaN -NaN
> > 9: vs pos=-NaN -NaN -NaN
> >
> > code_info: ESPResSo-3.2.0
> > { Compilation status { FFTW } { CUDA } { VIRTUAL_SITES_COM } }