Create_atoms command for atom/molecule mixture

LAMMPS LAMMPS General Discussion
1

Dear all
I try to build a simulation box mixing 1 atome type and a mole cule
I write.
molecule Gly glycerol_753.txt
region mybox block 0 50 0 50 0 30
create_box 4 mybox
create_atoms 4 random 50 78913542 mybox overlap 3.0 maxtry 50
create_atoms offset mol Gly random 5 24897364 mybox overlap 3.0 maxtry 50

I read in the manual:

  • type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
    so I used offset as type

But I got the following error, meaning aan integer is required for type ?:

D:\MD\Pt-Glycerol> lmp -in Pt-Gly_GAS.in
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Loaded 1 plugins from C:\Users\pascal.brault\AppData\Local\LAMMPS 64-bit 2023-04-10-MSMPI\plugins
Loaded 1 plugins from C:\Users\pascal.brault\AppData\Local\LAMMPS USER-REBOMOS Plugin 28Mar2023-MSMPI
Loaded 1 plugins from C:\Users\pascal.brault\AppData\Local\LAMMPS ML-PACE Plugin 28Mar2023-MSMPI
Loaded 1 plugins from C:\Users\pascal.brault\AppData\Local\LAMMPS USER-AEAM Plugin 28Mar2023-MSMPI
units real
dimension 3
boundary p p p
atom_style charge

log logPtGlynvt.lammps
molecule Gly glycerol_753.txt
Read molecule template Gly:
1 molecules
0 fragments
14 atoms with max type 3
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region mybox block 0 50 0 50 0 30
create_box 4 mybox
Created orthogonal box = (0 0 0) to (50 50 30)
1 by 1 by 1 MPI processor grid
create_atoms 4 random 50 78913542 mybox overlap 3.0 maxtry 50
Created 50 atoms
using lattice units in orthogonal box = (0 0 0) to (50 50 30)
create_atoms CPU = 0.001 seconds
create_atoms offset mol Gly random 5 24897364 mybox overlap 3.0 maxtry 50
ERROR: Expected integer parameter instead of ‘offset’ in input script or data file (src/create_atoms.cpp:92)
Last command: create_atoms offset mol Gly random 5 24897364 mybox overlap 3.0 maxtry 50
PS D:\MD\Pt-Glycerol>

I do not find what is wrong in my script ?
Thanks a lot in advance
Pascal

2

Hello,
‘offset’ must be an integer, its the number by which the atom ids in the molecule template must be shifted.
Best,
Simon

3

Thanks a lot
This is what I do not understand;
I have 4 atom
type 1 2 3 are for those of the molecules and stands for C H O real atoms.
And type 4 stands for Pt atom which is randomly placed in the box.
if offset is one, I understand that types 1 2 3 become 2 3 4 ? And do not understand the meaning of these renumbered types ?
Thanks a lot for your help.

4

If the indexes in the molecule file already correspond to the final expected indexes, then you can use an offset of 0. Would that work for you ?

5

Unfortunately no when replacing offset by 0 I got the error following message
create_atoms 0 mol Gly random 5 24897364 mybox overlap 3.0 maxtry 50
ERROR: Unknown create_atoms command option mol (src/create_atoms.cpp:137)
Last command: create_atoms 0 mol Gly random 5 24897364 mybox overlap 3.0 maxtry 50
PS D:\MD\Pt-Glycerol>

6

Indeed the command is still wrong, you have to pick a style first. ‘mol’ is a keyword, and it comes after the style.

Here you can just bring ‘random 5 24897364’ before ‘mol Gly’.

7

Yes. Thanks a lot I was just seeing the same when re-reading the manual.
Thanks again. And all is always in the manual :slight_smile:

8

Great it works when the ordering t is the good one.
Thanks again @simongravelle