create_bond not working to create Si tetrahedron. ERROR: Illegal create_bonds command (../create_bonds.cpp:45)

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1

Dear users,

I am using LAMMPS (30 Jul 2016) version.

I was trying to create a silcon tertrahedron with 1 silicon atom bonded with 4 oxygen atom (3 basal and 1 at apical position) using lattice command.

When i am trying to create bond using,

create_bond command single/bond 1 1 5

where first argument is bond type one and between atom no 1(oxygen) and 5 (silicon), i always get illegal bond error.

ERROR: Illegal create_bonds command (…/create_bonds.cpp:45)

I tried many style also but nothing is working out.
Can it be version problem or some patch missing problem.

Any guidance is highly appreciated.

Regards,
Ashwani

input file (1.38 KB)

log.lammps (1.43 KB)

2

Dear users,

I am using LAMMPS (30 Jul 2016) version.

I was trying to create a silcon tertrahedron with 1 silicon atom bonded with 4 oxygen atom (3 basal and 1 at apical position) using lattice command.

When i am trying to create bond using,

create_bond command single/bond 1 1 5

where first argument is bond type one and between atom no 1(oxygen) and 5 (silicon), i always get illegal bond error.

ERROR: Illegal create_bonds command (…/create_bonds.cpp:45)

I tried many style also but nothing is working out.
Can it be version problem or some patch missing problem.

​the error message means, that you are not using the syntax for the create_bonds command correctly.
the command line you quoted cannot work, since the name of the command is “create_bonds” not “create_bond”, also there is no “command” keyword.

you can easily figure out the correct syntax for your LAMMPS version by looking at the copy of the manual, that is bundled with your LAMMPS version.
the online manual always represents the very latest version of LAMMPS.

axel.​

3

Apologies for not able to explain my query in correct way or order. I want to create a silicon tetrahedron with one silicon bonded with four oxygen atom. create_bond command is not working at all to create Si-O bond. As you can see my input file that I have used syntax correctly still same error is coming. Since bond are not created, hence angle creation is also affected,I am using LAMMPS (30 Jul 2016) version. First four basis are for oxygen atom and last one is oxygen. I wanted to create only one type of bond and angle.

echo both

units real

atom_style full

pair_style lj/class2/coul/cut 1 1
bond_style class2
angle_style class2
boundary p p p

lattice custom 1 &
a1 5.14 0 0 &
a2 0 8.93 0 &
a3 0 0 7.37 &
basis 0.629 0.8 0.99 &
basis 0.999 0.631 0 &
basis 0.947 0.99 0 &
basis 0 0.8 0 &
basis 0.631 0.8 0.25

region myreg block 0 2 0 2 0 2

create_box 2 myreg bond/types 1 extra/bond/per/atom 6 angle/types 1 extra/bond/per/atom 6 extra/angle/per/atom 8

create_atoms 2 region myreg basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 2 units lattice

pair_modify tail yes
neighbor 2 bin
neigh_modify every 1000 delay 0 check yes page 100000 one 10000

replicate 1 1 1

mass 1 16
mass 2 32

pair_coeff 1 1 .2280 3.210 #O-O
pair_coeff 2 2 0.04001 4.550 #Si-Si
pair_coeff 1 2 0.10126 3.8217

bond_coeff 1 1.0 100.0 80.0 80.0

angle_coeff 1 110.6 88.1 -57 92.5
angle_coeff 1 bb 0 0 0
angle_coeff 1 ba 0 0 0 0

create_bonds single/bond 1 1 5
create_bonds single/bond 1 2 5

create_bonds single/bond 1 3 5
create_bonds single/bond 1 4 5

create_bonds single/angle 1 1 5 2
create_bonds single/angle 1 1 5 3
create_bonds single/angle 1 1 5 4
create_bonds single/angle 1 4 5 2
create_bonds single/angle 1 4 5 3
create_bonds single/angle 1 2 5 3

dump 1 all custom 10000 rev.* id x y z

timestep .01
run_style verlet

fix 1 all npt temp 298 298 1000 iso 1 1 10000

thermo_style custom step lx ly lz epair ebond eangle edihed etotal temp density
thermo 2000

run 100000

ERROR: Illegal create_bonds command (…/create_bonds.cpp:45) just after line create_bonds single/bond 1 1 5 .

I am confident its not any syntax error. I think i am missing some genuine point which i am not able to figure out. Any help is highly appreciable.

Ashwani

4

Apologies for not able to explain my query in correct way or order. I want to create a silicon tetrahedron with one silicon bonded with four oxygen atom. create_bond command is not working at all to create Si-O bond. As you can see my input file that I have used syntax correctly still same error is coming.

​you have not read the documentation for your specific version, as i instructed you to do. the options you are using are not pre​sent in your version.

​axel.​

Since bond are not created, hence angle creation is also affected,I am using LAMMPS (30 Jul 2016) version. First four basis are for oxygen atom and last one is oxygen. I wanted to create only one type of bond and angle.

echo both

units real

atom_style full

pair_style lj/class2/coul/cut 1 1

​1.0 angstrom default cuto​ff of LJ and coulomb, you must be joking.