Hello,
I have been trying to make wrinkle free graphene sheet. I have created a graphene sheet (8nm X 8nm) using Nanotube builder in VMD. From the obtained pdb file I have successfully created lammps data file using VMD Topotools. To avoid the wrinkle effect I have manually added the bonds between the corresponding edge atoms along both x and y directions at the end of the bonds, angles and dihedral sections of the data file manually.
Now when I try to run the simulations I am getting the following error :
echo screen
orthogonal box = (-40.6331 -40.5263 -59.786) to (40.3978 40.2957 59.674)
2 by 1 by 2 MPI processor grid
reading atoms …
59575 atoms
scanning bonds …
4 = max bonds/atom
ERROR: Unknown identifier in data file: 1 7 2 1 6 (…/read_data.cpp:391)
As soon as the program tries to read the first line in angle sections it gives the following error. Can you kindly let me know what exactly is causing this error.
I have attached the data file for your reference.
Thanks in advance for your kind help.
Regards,
GRP_EL_LI_PS_infinite.data (10.6 MB)
Hello,
I have been trying to make wrinkle free graphene sheet. I have created a
graphene sheet (8nm X 8nm) using Nanotube builder in VMD. From the obtained
pdb file I have successfully created lammps data file using VMD Topotools.
To avoid the wrinkle effect I have manually added the bonds between the
corresponding edge atoms along both x and y directions at the end of the
bonds, angles and dihedral sections of the data file manually.
Now when I try to run the simulations I am getting the following error :
echo screen
orthogonal box = (-40.6331 -40.5263 -59.786) to (40.3978 40.2957 59.674)
2 by 1 by 2 MPI processor grid
reading atoms ...
59575 atoms
scanning bonds ...
4 = max bonds/atom
ERROR: Unknown identifier in data file: 1 7 2 1 6 (../read_data.cpp:391)
this kind of message usually means that your data file is either
consistent, i.e. its header claims a different number of
atoms/bonds/angles/dihedrals than the corresponding sections have, or
that your atoms style in the input is different from the one used to
create the data file.
axel.
Thanks a lot the information. I checked the data file and it seems there was a numbering error in the bond, angle and diherdral list. Now I am not that error any more.
But I am geting a following error:
LAMMPS (10 Aug 2015)
units real
dimension 3
atom_style full
boundary p p p
read_data GRP_EL_LI_PS_infinite.data
Reading data file ...
orthogonal box = (-45.8005 -45.6796 -21.4674) to (46.3003 46.1704 20.8826)
4 by 3 by 2 MPI processor grid
reading atoms ...
20733 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
reading bonds ...
21403 bonds
reading angles ...
38619 angles
reading dihedrals ...
43431 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
Special bond factors lj: 0 0 0
Special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
Thanks a lot the information. I checked the data file and it seems there was a numbering error in the bond, angle and diherdral list. Now I am not that error any more.
But I am geting a following error:
LAMMPS (10 Aug 2015)
units real
[...]
--------------------------------------------------------------------------
ERROR on proc 18: 1-3 bond count is inconsistent (../special.cpp:299)
ERROR on proc 22: 1-3 bond count is inconsistent (../special.cpp:299)
Does this error means that the number of angle or dihedrals that I have added manually does not match the number that needs to be present consistent with the additional bonds specified?
no, but there seem to be some inconsistencies in the data. most
likely, some of the bonds/angles/dihedrals you added manually are not
correct.
there is one question that i keep wondering about: if you are having
so much trouble creating this additional topology information, and
considering that you're going to be using a rather crude model for
your system anyway, why don't you may your life a whole lot simpler by
using a potential like AIREBO that computes all of this topology data
on the fly, so you just need to provide a data file with the atom
coordinates only?
axel.
Thanks a lot for the information. I will check the data file for any errors. I am going to use AIREBO potential but at a later stage, initially I want to use only OPLS to study certain properties.
Thanks for your guidance.
Regards,
Aniruddha M Dive
PhD student
School of Mechanical and Materials Engg.
Washington State University