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 } }