LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] create_atoms and molecule command
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] create_atoms and molecule command


From: "Jie Wang" <wjnankai@...127...>
Date: Tue, 22 May 2018 17:35:51 +0800 (CST)

Dear all,
       I create a period box with lammps and the input file as follows:

units real

atom_style charge

#     reax args: hbcut hbnewflag tripflag precision

region         mybox prism 0.0 30.9713 0.0 26.8219 0.0 31.3220 -15.4856 0.0 0.0
create_box     1 mybox
molecule       O2 molecule.txt
create_atoms   1 random 10 100001 mybox mol O2 100000001
pair_style      reax/c lmp_control
pair_coeff      * * ffield.reax O

neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
timestep 0.25
fix             1 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 2 all nvt temp 100.0 100.0 25.0

thermo 10
dump            1 all custom 10 dump.custom id element x y z
dump_modify     1 element O format float %15.8f


run 100
the molecule.txt is shown as follows:
#O2

2 atoms

Coords

1       0.87719297    1.12573098    0.00000000
2      -0.28440703    1.12573098    0.00000000

Types

1 1
2 1

Masses

1 15.9990
2 15.9990
But the error occurs:
Created triclinic box = (0 0 0) to (30.9713 26.8219 31.322) with tilt (-15.4856 0 0)
  1 by 1 by 2 MPI processor grid
Read molecule O2:
  2 atoms with 2 types
  0 bonds with 0 types
  0 angles with 0 types
  0 dihedrals with 0 types
  0 impropers with 0 types
ERROR: Invalid atom type in create_atoms mol command (../create_atoms.cpp:217)
Last command: create_atoms   2 random 10 100001 mybox mol O2 100000001
Could you tell me how to correct it? Thanks.
                                    Best regards,
            Jie Wang