Dear all,
My apologies if that has already been discussed and fixed,
but I can't find anything like that in archives.
I would like to use "copy_particles" procedure so that it
could copy both bonds and exclusions. There was a question
about it and there is a file on Github, that basically fixes
it up. But even if I use the last version of "auxiliary.tcl"
there is still a little problem with "fix" parameter. I
attache a simple example below.
1.We are just putting few particles into the box and adding
some interactions.
setmd box_l 100 100 100
setmd time_step 0.001
setmd skin 0.5
inter 0 1 lennard-jones 1.0 1.0 1.26 1.0 0.0 0.0
inter 1 2 lennard-jones 1.0 1.0 1.26 1.0 0.0 0.0
inter 4 HARMONIC 4000.0 1.0
thermostat langevin 0.0 1.0
part 0 pos 1.0 1.0 1.0 type 0
part 1 pos 2.0 1.0 1.0 type 1
part 2 pos 3.0 1.0 1.0 type 2 fix 1 1 1
part 0 bond 4 1
part 1 bond 4 2
2. Then we're excluding one of non-bonded interactions
part 2 exclude 1
3.And, finally, using the "copy_particles"
copy_particles range 0 2 shift 0.0 2.0 0.0
integrate 100
puts [part]
puts [analyze energy]
The problem appears on the 3rd step when I'm trying to
copy a fixed particle with exclusions.
unknown particle parameter "1"
while executing
"part 5 pos 3.0 3.0 1.0 type 2 mass 1.0 q 0.0 v 0.0 0.0
0.0 f 0.0 0.0 0.0 quat 1.0 0.0 0.0 0.0 omega 0.0 0.0 0.0
torque 0.0 0.0 0.0 virtual 0 vs_relati..."
("eval" body line 1)
invoked from within
"eval part $newid $partcmd"
(procedure "copy_particles" line 62)
invoked from within
"copy_particles range 0 2 shift 0.0 2.0 0.0"
It's about the first 1 in the "fix 1 1 1".
If I delete the "fix" argument, everything seems to be
ok.
Looks like it is really simple, but I can't figure it
out.
Hope someone can clear it up.
Thank in advance!
--
Kind regards,
Aleksei
auxiliary.tcl