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

[Olaf Lenz]

Hi Tristan!

Did you get a reply to this mailing off-list?

Olaf

On 02/08/2013 10:20 AM, Tristan Bereau wrote:
> 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 } }
> 


-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

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