[ESPResSo-users] Can't get virtual sites to work

[Tristan Bereau]

Dear all,

This must be a stupid mistake on my part, but I can't seem to spot it.
I was trying to setup an example script to work with virtual sites
(defined with respect to the center of mass of the molecule,
VIRTUAL_SITES_COM). I set up two molecules of two particles each and
define their virtual sites by the following script:

part 0 pos  0.0  0.0 0.0 mol 1
part 1 pos  1.0  1.0 0.0 mol 1
part 2 pos  9.0  9.0 9.0 mol 1 virtual 1
part 3 pos  5.5  0.0 2.0 mol 2
part 4 pos  4.5  1.0 2.0 mol 2
part 5 pos  8.0  8.0 8.0 mol 2 virtual 1
analyze set 1 "0 1 2" 2 "3 4 5"
puts "call 'analyze set': [analyze set]"

foreach i [part] { puts $i }
puts ""
setmd time_step 0.001; thermostat off; setmd skin 1.0

puts "call 'integrate 1'"
integrate 1

foreach i [part] { puts $i }

puts "\ncode_info: [code_info]"

*************

The output is below. As you can see, the call to "integrate 1" does
not properly place virtual site 1 (it stays at its initial position)
and virtual site 2 becomes NaN. Could anyone tell me what I'm doing
wrong?

Thanks,
Tristan



call 'analyze set': { 1 } { 0 1 2 } { 2 } { 3 4 5 }
0 pos 0.0 0.0 0.0 type 0 molecule 1 mass 1.0 v -0.0 -0.0 -0.0 f 0.0
0.0 0.0 virtual 0
1 pos 1.0 1.0 0.0 type 0 molecule 1 mass 1.0 v -0.0 -0.0 -0.0 f 0.0
0.0 0.0 virtual 0
2 pos 9.0 9.0 9.0 type 0 molecule 1 mass 1.0 v -0.0 -0.0 -0.0 f 0.0
0.0 0.0 virtual 1
3 pos 5.5 0.0 2.0 type 0 molecule 2 mass 1.0 v -0.0 -0.0 -0.0 f 0.0
0.0 0.0 virtual 0
4 pos 4.5 1.0 2.0 type 0 molecule 2 mass 1.0 v -0.0 -0.0 -0.0 f 0.0
0.0 0.0 virtual 0
5 pos 8.0 8.0 8.0 type 0 molecule 2 mass 1.0 v -0.0 -0.0 -0.0 f 0.0
0.0 0.0 virtual 1

call 'integrate 1'
0 pos 0.0 0.0 0.0 type 0 molecule 1 mass 1.0 v 0.0 0.0 0.0 f 0.0 0.0
0.0 virtual 0
1 pos 1.0 1.0 0.0 type 0 molecule 1 mass 1.0 v 0.0 0.0 0.0 f 0.0 0.0
0.0 virtual 0
2 pos 9.0 9.0 9.0 type 0 molecule 1 mass 1.0 v 0.0 0.0 0.0 f 0.0 0.0
0.0 virtual 1
3 pos 5.5 0.0 2.0 type 0 molecule 2 mass 1.0 v 0.0 0.0 0.0 f 0.0 0.0
0.0 virtual 0
4 pos 4.5 1.0 2.0 type 0 molecule 2 mass 1.0 v 0.0 0.0 0.0 f 0.0 0.0
0.0 virtual 0
5 pos -nan -nan -nan type 0 molecule 2 mass 1.0 v -nan -nan -nan f 0.0
0.0 0.0 virtual 1

code_info: ESPResSo-3.1.1
{ Compilation status { FFTW } { CONSTRAINTS } { BOND_ANGLE_HARMONIC }
{ COMFIXED } { NPT } { COMFORCE } { PARTIAL_PERIODIC } { LENNARD_JONES
} { LJ_ANGLE } { OVERLAPPED } { MODES } { EXTERNAL_FORCES } {
TABULATED } { METADYNAMICS } { LJCOS } { LENNARD_JONES_GENERIC } {
MASS } { MOLFORCES } { LJCOS2 } { DPD } { VIRTUAL_SITES_COM } {
BOND_VIRTUAL } { LJ_WARN_WHEN_CLOSE } { EXCLUSIONS } }