create-box mol /topology error

Dear lammps users,

I using lammps nov16 version. I am trying to create a system containing carbon dioxide molecules only. my input file and CO2 file are below, however , I am keep receiving this error ERROR: Molecule topology/atom exceeds system topology/atom (…/molecule.cpp:1398). I thought this might be coming from the special bond section. Therefore, I tried to run the simulation to remove after removing the special bonds and special bond count section. However, I received the error

units real

dimension 3

boundary p p p

atom_style full

region box block 0 300 0 300 0 300

create_box 2 box bond/types 1 angle/types 1 extra/special/per/atom 2

Created orthogonal box = (0 0 0) to (300 300 300)

2 by 2 by 4 MPI processor grid

molecule co2 co1

Read molecule co2:

3 atoms with 2 types

2 bonds with 1 types

1 angles with 1 types

0 dihedrals with 0 types

0 impropers with 0 types

create_atoms 0 random 1000 25 box mol co2 25

ERROR: Molecule toplogy/atom exceeds system topology/atom (…/molecule.cpp:1398)

File

3 atoms

2 bonds

1 angles

Coords

1 0.0 0.0 0.0

2 -1.163 0.0 0.0

3 1.163 0.0 0.0

Types

1 1

2 2

3 2

Charges

1 0.6645

2 -0.33275

3 -0.33275

Bonds

1 1 1 2

2 1 1 3

Angles

1 1 2 1 3

Special Bond Counts

1 2 0 0

2 1 0 0

3 1 0 0

Special Bonds

1 2 3

2 1

3 1

Input file

Initialization

units real

dimension 3

boundary p p p

atom_style full

region box block 0 300 0 300 0 300

create_box 2 box bond/types 1 angle/types 1 extra/special/per/atom 2

molecule co2 co1

create_atoms 0 random 1000 25 box mol co2 25

Dear lammps users,

I using lammps nov16 version. I am trying to create a system containing
carbon dioxide molecules only. my input file and CO2 file are below,
however , I am keep receiving this error ERROR: Molecule topology/atom
exceeds system topology/atom (../molecule.cpp:1398). I thought this might
be coming from the special bond section. Therefore, I tried to run the
simulation to remove after removing the special bonds and special bond
count section. However, I received the error

​yes, because you don't reserve storage for bonds and angles, which are
stored with atoms, that "own" then.
so you need to add a suitable extra/bond/per/atom and extra/angle/per/atom
flag to create_box.

axel.​

thanks sir,
I modified my input and it works fine for CO2. however, when i defined octane molecule ( file attached below) and defined my box by the following command
create_box 2 box extra/bond/per/atom 2 extra/angle/per/atom 3 extra/dihedral/per/atom 3

I received this error
ERROR on proc 0: Molecule auto special bond generation overflow (…/molecule.cpp:1155)

octane
regards

0.lmp (3.57 KB)

thanks sir,
I modified my input and it works fine for CO2. however, when i defined
octane molecule ( file attached below) and defined my box by the following
command
create_box 2 box extra/bond/per/atom 2 extra/angle/per/atom 3
extra/dihedral/per/atom 3

I received this error
ERROR on proc 0: Molecule auto special bond generation overflow
(../molecule.cpp:1155)

thanks ,sir
does this mean molecule command can not handle larger molecule with many special bonds?
i rerun my system with extra/special/per/atom set to large number and i received another ERORR Molecule topology type exceeds system topology type (…/molecule.cpp:1381)
thanks

thanks ,sir
does this mean molecule command can not handle larger molecule with many
special bonds?

​no, it can.​

i rerun my system with extra/special/per/atom set to large number and i
received another ERORR Molecule topology type exceeds system topology type
(../molecule.cpp:1381)

​are you now going to quote *every​* error five seconds after you
encountered it, rather than looking at the manual and the documentation of
the related to commands to make an effort to understand and correct your
mistakes?

that is what a documentation is written for. if you unable to figure out
how to build a proper system with the molecule command (which can be
cumbersome at times, especially when one doesn't pay attention to the
documentation and review errors and what is happening inside of LAMMPS due
to the commands executed), then there is always the option to build a
topology and data file with external tools.

nobody here has the time to spoonfeed you what you can sort out by yourself
with a little bit of effort, thinking and common sense.

axel.

thanks
and i really appreciate any reply
regards