Dear Sirs
I am a beginner in LAMMPS. Now I am trying to simulate fragmentation
of large size Graphite into small size(Graphene). System is like
that…..Graphite will come onto fixed Cu substrate
with supersonic velocity in vacuum condition and at room temperature.
I have written some code to run but facing error message…ERROR: Lost
atoms : Original 107440 current 107439
(../thermo.cpp:389) My input structure of is large 107440 atoms. I
tried with enlarging the simulation Box, decreasing the time step as
well as reducing the Graphite velocity. But still now I am getting
this error
message. Here I am attaching the log file and input script. Is there
anybody who are working in such kind of simulation, or help me by
giving suggestion to solve this error message or sending
me the related input file.
# LAMMPS Input File
# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p f
atom_style atomic
# ---------- Create Atomistic Structure ---------------------
lattice fcc 1.0
read_data Cu_graph.dat
group substrate type 1
group graphite type 2
group bottom type 3
fix b2 bottom setforce 0.0 0.0 0.0
# ---------- Define Interatomic Potential ---------------------
pair_style hybrid eam lj/cut 4.0 airebo 3.0 0 0
pair_coeff * * airebo CH.airebo NULL C NULL
pair_coeff 1 1 eam Cu_u3.eam
pair_coeff 3 3 eam Cu_u3.eam
pair_coeff 1 2 lj/cut 0.0042038 3.37
pair_coeff 1 3 none
pair_coeff 2 3 none
neighbor 2.0 bin
neigh_modify delay 10 check yes
# ---------- Run Minimization ---------------------
reset_timestep 0
timestep 0.001
thermo 10
thermo_style custom step temp press pe ke etotal enthalpy
dump 1 all xyz 500 newfrag1.xyz
velocity graphite set 0.0 0.0 -3.2
fix 10 all nve
run 20000
Regards
Nasim
Modifysystem.txt (988 Bytes)
log.lammps (3.79 KB)
Dear Nasim
Atoms are scraping through you finite z boundary. I can't figure out why you need it. Make it p instead of f and you no longer will have such an error.
Best,
Alan
Hi Alan
I tried with p boundary condition for z axis. I need to set it as f or
s, because in another case for small structure when I tried with p
boundary
condition for z axis I found some layers of Graphite appeared below
the substrate which is not expected. Is there any coments? Please let
me know.
Regards
Nasim
Hi Alan
I tried with p boundary condition for z axis. I need to set it as f or
s, because in another case for small structure when I tried with p
boundary
condition for z axis I found some layers of Graphite appeared below
the substrate which is not expected. Is there any coments? Please let
me know.
you have to know what kind of system exactly you want to model, and
that decides what boundary conditions (or other system parameters) you
need to choose.
when atoms get pushed out of the plane with periodic boundaries, that
means that you have close contacts across the periodic boundaries,
i.e. atoms get unphysically close, or you have a system drift, which
is equally unphysical and usually an artifact of bad initial
velocities or otherwise badly chose simulation parameters.
both topics have been discussed on this very mailing list, many, many
times. they apply to many simulations and are typical beginner
problems, indicating a lack of training.
so please start by doing a thorough search through the mailing
archives and have a chat or two with whoever is advising you on
setting up MD simulations. this kind of advising should have covered
such trivial issues.
axel.
First, check the official documentation:
http://lammps.sandia.gov/doc/Section_errors.html
It says:
"Lost atoms usually indicate bad dynamics, e.g. atoms have been blown
far out of the simulation box"
The same goes for lost angles, lost bonds, etc..
Axel has a point. Google this:
LAMMPS error lost atoms
and you will get a lot of links.
README_visualize.txt (2.85 KB)
Dear Sirs
Thanks for your good advice. I solved the previous problem. I found
one atom was overlapping. Now it is ok. But another problem is......
I am facing ERROR: Incorrect args for pair coefficients
(../pair_eam.cpp:389) I have 3 types atoms. 1,2 and 3. Type 1 is
graphite, 2 & 3 are Cu.
Type 3 is fixed bottom part of substrate. Would you please tell me
exactly where I am doing wrong?and for interaction between Cu and
graphite I am using
lj potential. Still now I don't have any referance for that potential.
I badly need it.............here is my input file
# LAMMPS Input File
# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p f
atom_style atomic
# ---------- Create Atomistic Structure ---------------------
lattice fcc 1.0
read_data Cu_graph.dat
group graphite type 1
group substrate type 2
group bottom type 3
fix b2 bottom setforce 0.0 0.0 0.0
# ---------- Define Interatomic Potential ---------------------
pair_style hybrid eam lj/cut 4.0 airebo 3.0 0 0
pair_coeff * * airebo CH.airebo NULL C NULL
pair_coeff 2 2 eam Cu_u3.eam
pair_coeff 3 3 eam Cu_u3.eam
pair_coeff 1 2 lj/cut 0.0042038 3.37
pair_coeff 1 3 lj/cut 0.0042038 3.37
pair_coeff 2 3 eam Cu_u3.eam
neighbor 2.0 bin
neigh_modify delay 10 check yes
# ---------- Run Minimization ---------------------
reset_timestep 0
timestep 0.001
thermo 10
thermo_style custom step temp press pe ke etotal enthalpy
minimize 1e-10 1e-10 1000 1000
dump 1 all xyz 500 newfrag3.xyz
velocity graphite set 0.0 0.0 -3.2
fix 10 all nve
run 20000
Regards
Nasim
You need to use “pair_coeff * * …” for eam. Please have a look at eam’s doc page for more info.
Ray