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[ESPResSo-users] Can't get virtual sites to work
From: |
Tristan Bereau |
Subject: |
[ESPResSo-users] Can't get virtual sites to work |
Date: |
Fri, 8 Feb 2013 10:20:28 +0100 |
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 } }
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