Hi,
I am getting the following error when i run my lammps input script that uses OpenKIM potential:
WARNING: ‘kim_’ has been renamed to ‘kim ’. Please update your input.
ERROR: Unknown command: kim init Tersoff_LAMMPS_Tersoff_1988_C__MO_579868029681_003 metal (src/input.cpp:391)
Attaching the LAMMPS input file herewith.
cnt_tersoff.in (2.3 KB)
Please let us know your exact LAMMPS version.
LAMMPS version: 20191120+dfsg1-2build2
That is too old.
Oh, I see. I have installed LAMMPS using the pre-build Ubuntu Linux executable for the Ubuntu version 20.04.5 LTS. When i use
sudo apt-get update
to update the LAMMPS version, the version i get is 20191120+dfsg1-2build2
How do i obtain the latest LAMMPS version for my OS then?
You have three options:
There is a fourth option: update to Ubuntu 22.04LTS. That one seems to ship with the 29 Sep 2021 version. While that is not the latest, it is two years more recent that the one for Ubuntu 20.04LTS.
I have updated my LAMMPS version by building from source. Still getting the same error:
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
ERROR: Unknown command: kim init Tersoff_LAMMPS_Tersoff_1988_C__MO_579868029681_003 metal (src/input.cpp:302)
Last command: kim init Tersoff_LAMMPS_Tersoff_1988_C__MO_579868029681_003 metal
Traceback (most recent call last):
It works for me. Did you compile LAMMPS with the Kim package enabled? What is the output of: lmp - h
Is the input still exactly the same as in your original post?
Not sure about the first question.
Output of lmp -h:
Large-scale Atomic/Molecular Massively Parallel Simulator - 23 Jun 2022 - Update 1
Git info (stable / stable_23Jun2022_update1)
Usage example: lmp -var t 300 -echo screen -in in.alloy
List of command line options supported by this LAMMPS executable:
-echo none/screen/log/both : echoing of input script (-e)
-help : print this help message (-h)
-in none/filename : read input from file or stdin (default) (-i)
-kokkos on/off ... : turn KOKKOS mode on or off (-k)
-log none/filename : where to send log output (-l)
-mdi '<mdi flags>' : pass flags to the MolSSI Driver Interface
-mpicolor color : which exe in a multi-exe mpirun cmd (-m)
-cite : select citation reminder style (-c)
-nocite : disable citation reminder (-nc)
-package style ... : invoke package command (-pk)
-partition size1 size2 ... : assign partition sizes (-p)
-plog basename : basename for partition logs (-pl)
-pscreen basename : basename for partition screens (-ps)
-restart2data rfile dfile ... : convert restart to data file (-r2data)
-restart2dump rfile dgroup dstyle dfile ...
: convert restart to dump file (-r2dump)
-reorder topology-specs : processor reordering (-r)
-screen none/filename : where to send screen output (-sc)
-skiprun : skip loops in run and minimize (-sr)
-suffix gpu/intel/opt/omp : style suffix to apply (-sf)
-var varname value : set index style variable (-v)
OS: Linux "Ubuntu 20.04.5 LTS" 5.15.0-46-generic x86_64
Compiler: GNU C++ 9.4.0 with OpenMP 4.5
C++ standard: C++11
MPI v3.1: Open MPI v4.0.3, package: Debian OpenMPI, ident: 4.0.3, repo rev: v4.0.3, Mar 03, 2020
Accelerator configuration:
Active compile time flags:
-DLAMMPS_GZIP
-DLAMMPS_PNG
-DLAMMPS_JPEG
-DLAMMPS_SMALLBIG
sizeof(smallint): 32-bit
sizeof(imageint): 32-bit
sizeof(tagint): 32-bit
sizeof(bigint): 64-bit
Available compression formats:
Extension: .gz Command: gzip
Extension: .bz2 Command: bzip2
Extension: .xz Command: xz
Extension: .lzma Command: xz
Extension: .lz4 Command: lz4
Installed packages:
List of individual style options included in this LAMMPS executable
* Atom styles:
atomic body charge ellipsoid hybrid
line sphere tri
* Integrate styles:
respa verlet
* Minimize styles:
cg fire fire/old hftn quickmin
sd
* Pair styles:
born buck buck/coul/cut coul/cut coul/debye
coul/dsf coul/wolf reax hybrid hybrid/overlay
hybrid/scaled lj/cut lj/cut/coul/cut lj/expand morse
soft table yukawa zbl zero
* Bond styles:
hybrid zero
* Angle styles:
hybrid zero
* Dihedral styles:
hybrid zero
* Improper styles:
hybrid zero
* KSpace styles:
* Fix styles
adapt addforce ave/atom ave/chunk ave/correlate
ave/histo ave/histo/weight ave/time aveforce
balance box/relax deform deposit ave/spatial
ave/spatial/sphere lb/pc lb/rigid/pc/sphere
client/md dt/reset efield enforce2d evaporate
external gravity halt heat indent
langevin lineforce momentum move nph
nph/sphere npt npt/sphere nve nve/limit
nve/noforce nve/sphere nvt nvt/sllod nvt/sphere
planeforce press/berendsen print property/atom recenter
restrain setforce spring spring/chunk spring/self
store/force store/state temp/berendsen temp/rescale
thermal/conductivity vector viscous wall/harmonic
wall/lj1043 wall/lj126 wall/lj93 wall/morse wall/reflect
wall/region
* Compute styles:
aggregate/atom angle angle/local angmom/chunk bond
bond/local centro/atom centroid/stress/atom chunk/atom
chunk/spread/atom cluster/atom cna/atom com
com/chunk coord/atom dihedral dihedral/local dipole
dipole/chunk displace/atom erotate/sphere erotate/sphere/atom
fragment/atom global/atom group/group gyration gyration/chunk
heat/flux improper improper/local inertia/chunk ke
ke/atom msd msd/chunk omega/chunk orientorder/atom
pair pair/local pe pe/atom pressure
property/atom property/chunk property/local rdf reduce
reduce/chunk reduce/region slice stress/atom temp
temp/chunk temp/com temp/deform temp/partial temp/profile
temp/ramp temp/region temp/sphere torque/chunk vacf
vcm/chunk
* Region styles:
block cone cylinder ellipsoid intersect
plane prism sphere union
* Dump styles:
atom cfg custom image local
movie xyz
* Command styles
balance change_box create_atoms create_bonds create_box
delete_atoms delete_bonds reset_ids kim_init kim_interactions
kim_param kim_property kim_query message server
displace_atoms info minimize read_data read_dump
read_restart replicate rerun reset_atom_ids reset_mol_ids
run set velocity write_coeff write_data
write_dump write_restart
Yes the input file is the same.
Hi @imomnipresent, to clarify @akohlmey remark: the KIM package is an external package that is not necessary to compile LAMMPS. You need to specifically add it (and install kim-api and models).
See sections 3.1, 3.2 and 3.7 of the Build Section from the manual that @akohlmey already posted. Section 3.7 has a dedicated section on how to add kim package.
From you output it seems that the kim command and pair_style are absent from your executable so I do not think it was compiled with the package.
The lmp -h output confirms, there are no additional packages included in your LAMMPS binary and thus also not the KIM package. You need to enable it (and first activate your kim-api installation so CMake can detect it) and then recompile LAMMPS. 3.7. Packages with extra build options — LAMMPS documentation
When you recompile, it is usually a good idea to add the “basic packages preset” to also install a few packages with the most commonly used features beyond the absolute minimum or the “most packages preset” with most packages that do not need extra setup or external libraries.