[lammps-users] some questions about fix deposite and airebo potential

Hi,
evergy body,I have some question while using the lammps.I would be very grateful if someone gives constructive advices.
(1)As i known, the command of fix deposite is only used with atoms. when i use the command to deposite clusters of CH3,how can i do it?
(2)The airebo potential in Lammps can now be used in high temperature runs? About a month ago, I asked the question about hi-temp runs (8000K) with airebo potential .
(3)the question i have asked a month ago which I still did not solved.
when i simulat the carbon atom deposited to the surface of diamond substrate,after one carbon atom collided with the surface, the TotEng changed slightly .but at some point, the sign of TotEng altered from negative(-14800.763) to positive (3796.5833). runing the same script with tersoff potential gives good results.

ERROR: Lost atoms: original 2188 current 2185
I don’t know the reason.is there some bug in the potentail of airebo ?
the input file:

echo both

initilization

units metal
dimension 3
boundary p p fm
atom_style atomic
#atom definition
lattice diamond 3.5667
region box1 block 0 8 0 8 0 20
create_box 4 box1
#neighbor 5.0 bin
#neigh_modify delay 0
#setting
mass 1 12.011150 # the mass of C
mass 2 12.011150 # the mass of C
mass 3 12.011150 # the mass of C
mass 4 12.011150 # the mass of C
#EAM potentials
pair_style airebo 2.5 0 0
pair_coeff * * CH.airebo C C C C

region box2 block 0 8 0 8 0 4
create_atoms 1 region box2

region 1 block INF INF INF INF INF 5 units box
region 2 block INF INF INF INF 5 10 units box
region 3 block INF INF INF INF 10 15 units box

group lower region 1
group constant region 2
group newdun region 3
group mobile union constant newdun

set group constant type 2
set group newdun type 3
#minimize 1.0e-6 1.0e-6 1000 1000
velocity mobile create 100.0 5812775 sum no
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 constant temp/rescale 10 100.0 100.0 1.0 1.0
compute 4 mobile temp
thermo_style custom step temp pe ke etotal press vol
thermo_modify temp 4
thermo 10
run 5000
group 44 type 4
group whole1 union mobile 44
thermo 1
fix 4 44 deposit 1 4 100 29494 region box2 vx 0.0 0.0 vy 0.0 0.0 vz -350.0 -350.0 attempt 50 global 10.0 10.0 units box
fix 6 all wall/reflect zlo zhi
compute 1 44 ke
compute 2 newdun temp
compute 3 constant temp
thermo_style custom step temp etotal c_1 c_2 c_3
dump 1 all xyz 10 cual.xyz
run 200
dump 2 all atom 100 dump.cual
run 30000

Comments below.

Steve

2010/10/13 黄德明 <[email protected]>:

Hi,
   evergy body,I have some question while using the lammps.I would be very
grateful if someone gives constructive advices.
(1)As i known, the command of fix deposite is only used with atoms. when i
use the command to deposite clusters of CH3,how can i do it?

you can't - someone would have to write a fix deposit/molecule.

(2)The airebo potential in Lammps can now be used in high temperature runs?
About a month ago, I asked the question about hi-temp runs (8000K) with
airebo potential .

Nothing significant has changed with AIREBO in the last month.
There are people investigating possible bugs with the LAMMPS
implementation of AIREBO, but I have received nothing concrete
from anyone to fix as of yet. That said, there are plenty of ways
to create and run bad simulations with LAMMPS, which are
user errors, not bugs, and it seems easier for the average user
to screw up AIREBO models than others.

(3)the question i have asked a month ago which I still did not solved.
when i simulat the carbon atom deposited to the surface of diamond
substrate,after one carbon atom collided with the surface, the TotEng
changed slightly .but at some point, the sign of
TotEng altered from negative(-14800.763) to positive (3796.5833). runing
the same script with tersoff potential gives good results.

ERROR: Lost atoms: original 2188 current 2185
I don't know the reason.is there some bug in the potentail of airebo ?
the input file:

This error is typically an indication of a user error due to a bad model.
See the answer above.