(no subject)

Hi all,

I was wandering what software do lammps users (in specific) use in order to design a difficult geomerty that they are using for their simulations? I mean ok CNTs is very popular and easy to develop a small code or use vmd for example. But in case someone wants something much more difficult what is the best approach ?

Regards
Jim

2012/1/5 Jim Jim <[email protected]...>:

Hi all,

I was wandering what software do lammps users (in specific) use in order to

wandering where? :wink:

design a difficult geomerty that they are using for their simulations? I
mean ok CNTs is very popular and easy to develop a small code or use vmd
for example. But in case someone wants something much more difficult what is
the best approach ?

there is no general solutions for this outside of bio systems,
since only those are simple chained polymers using only a
very limited number of components. beyond that, it is almost
always better to write something custom for your purposes
and don't bother to make it general.

the most general strategy for molecular systems that i can
think of would be using something like packmol to generate
initial coordinates and then VMD scripting or something
equivalent to generate the relevant topology information,
if at all needed.

axel.

Unfortunately everywhere… My main problem is that let’s say I want to make a CNT junction. There would be some points where the hexagonal structure becomes 7 from quantum optimization that at themoment I am not familiar and you can understand tht it is impossible to design it.
Thanks Axel.

Jim

Hi all,
I have done a simulation. but there is an error: Computed temperature for fix temp/rescale cannot be 0.0
the documentation of lammps says that :
Cannot rescale the temperature to a new value if the current temperature is 0.0.

but, how to solve this problem?

thank you in advance

It’s hard to tell you what you need to do to fix a problem if we don’t know what caused it in the first place. Did this happen in the middle of the simulation? At the very beginning? What kind of system were you simulating?

If it happened right at the start, then you probably didn’t assign atoms an initial temperature, and therefore temp/rescale won’t work. You’ll need to either use the “velocity” command or specify velocities for the atoms explicitly to fix that.

—AEI

i try to simulate hydrogen adsorption in CNT. i use this script :

3-d LJ hydrogen storage

dimension 3
boundary p p p

atom_style full
neighbor 0.5 bin
neigh_modify delay 5

read_data success5molekul.dat

#kspace_style ewald 1.0e-2
bond_style harmonic
bond_coeff 1 1201.1 0.254

LJ potentials

pair_style lj/cut/coul/cut 3.0
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.737 1.166
pair_coeff 1 2 1.858 1.083

Define groups

group cnt type 2
group hyd type 1

Initial velocities

compute mobile hyd temp
velocity hyd create 7.71037 482748 temp mobile
fix 1 all nve
fix 2 hyd temp/rescale 100 7.71037 7.71037 0.02 1.0
fix_modify 2 temp mobile

Static nanotube

velocity cnt set 0.0 0.0 0.0 units box
fix 3 cnt setforce 0.0 0.0 0.0
fix 4 cnt aveforce 0.0 0.0 0.0

Run

timestep 0.0003
thermo 10000
thermo_style custom step atoms temp pe ke evdwl
thermo_modify temp mobile

dump mydump all atom 10000 dump.successs
run 1000000

and the log.lammps like this :

LAMMPS (17 Jul 2010)

3-d LJ hydrogen storage

dimension 3
boundary p p p

atom_style full
neighbor 0.5 bin
neigh_modify delay 5

read_data success5molekul.dat
1 = max bonds/atom
orthogonal box = (-3.431 -3.431 -3.431) to (8.233 8.233 8.233)
1 by 1 by 1 processor grid
220 atoms
10 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors

#kspace_style ewald 1.0e-2
bond_style harmonic
bond_coeff 1 1201.1 0.254

LJ potentials

pair_style lj/cut/coul/cut 3.0
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.737 1.166
pair_coeff 1 2 1.858 1.083

Define groups

group cnt type 2
200 atoms in group cnt
group hyd type 1
20 atoms in group hyd

Initial velocities

compute mobile hyd temp
velocity hyd create 7.71037 482748 temp mobile
fix 1 all nve
fix 2 hyd temp/rescale 100 7.71037 7.71037 0.02 1.0
fix_modify 2 temp mobile

Static nanotube

velocity cnt set 0.0 0.0 0.0 units box
fix 3 cnt setforce 0.0 0.0 0.0
fix 4 cnt aveforce 0.0 0.0 0.0

Run

timestep 0.0003
thermo 10000
thermo_style custom step atoms temp pe ke evdwl
thermo_modify temp mobile

dump mydump all atom 10000 dump.successs
run 1000000
Memory usage per processor = 1.86589 Mbytes
Step Atoms Temp PotEng KinEng E_vdwl
0 220 7.71037 19970536 0.99884339 19970533
ERROR: Computed temperature for fix temp/rescale cannot be 0.0

Why don't you print out (with your thermo output) the
temp of the hyd group and see what it is. If it's zero,
then you can't temp/rescale it, b/c it divides by
the current temperature to get the new velocities.

Steve