Dear all,
I am a new user of LAMMPS. I did few basic simulations. I am now trying to simulate a layer of water in a simulation box. I keep getting the following error:
Molecule toplogy/atom exceeds system topology/atom (…/molecule.cpp:1419)
I understand that this error means the simulation box is not configured correctly to simulate the defined molecule. But I followed similar codes from previous emails in mailing list and I can’t see what is wrong. Can somebody please point out what is the mistake in my codes?
I attached the water molecule template I am using and I copied the relevant part of the input script below
Thank you for your help and time,
M. Hasan
Inputs script:
units real
atom_style full
dimension 3
boundary p p f
region MYBOX block 0 100 0 100 0 100
create_box 2 MYBOX bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
region LAYER block 0 100 0 100 0 50
molecule WATER H2O.txt
lattice sc 10
create_atoms 0 region LAYER mol WATER 361 # no extra atom types are needed hence 0
mass 1 15.9994
mass 2 1.00794
(the rest of the code…)
H2O.txt (370 Bytes)
Dear all,
I am a new user of LAMMPS. I did few basic simulations. I am now trying to
simulate a layer of water in a simulation box. I keep getting the following
error:
Molecule toplogy/atom exceeds system topology/atom (../molecule.cpp:1419)
I understand that this error means the simulation box is not configured
correctly to simulate the defined molecule. But I followed similar codes
from previous emails in mailing list and I can't see what is wrong. Can
somebody please point out what is the mistake in my codes?
your input works for me (see below). are you using a recent enough
version of LAMMPS?
axel.
LAMMPS (6 Jan 2017)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
dimension 3
boundary p p f
region MYBOX block 0 100 0 100 0 100
create_box 2 MYBOX bond/types 1 angle/types 1 extra/bond/per/atom 2
extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (100 100 100)
1 by 1 by 1 MPI processor grid
region LAYER block 0 100 0 100 0 50
molecule WATER H2O.txt
Read molecule WATER:
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
lattice sc 10
Lattice spacing in x,y,z = 10 10 10
create_atoms 0 region LAYER mol WATER 361 # no extra atom types are
needed hence 0
Created 1800 atoms
mass 1 15.9994
mass 2 1.00794
Total wall time: 0:00:00
Dear Axel,
Thank you for your reply,
I am running the code on a windows machine, the installer is the latest (dated 31-oct) and LAMMPS version associated with it is (27 Aug 2016-ICMS)
I just installed the latest version (17 Nov 2016) on a Linux machine and the code is working fine!!
Do you think when the latest version of LAMMPS becomes available on windows the problem will be resolved?
I appreciate your help,
M. Hasan
Dear Axel,
Thank you for your reply,
I am running the code on a windows machine, the installer is the latest (dated 31-oct) and LAMMPS version associated with it is (27 Aug 2016-ICMS)
I just installed the latest version (17 Nov 2016) on a Linux machine and the code is working fine!!
Do you think when the latest version of LAMMPS becomes available on windows the problem will be resolved?
yes.
you also should be be able to work around it by simply increasing the
reserved extra space of per atom topological data in your create_box
command.
axel.