Traceback (most recent call last): File "/disk2/worker/repository/td/ClusterEnergyAndForces__TD_000043093022_003/runner", line 47, in run_lammps ["lammps", '-in', infile], shell=False, stdout=outfl File "/usr/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['lammps', '-in', 'output/lammps_inputs/main.lammps.tpl']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/disk2/worker/repository/td/ClusterEnergyAndForces__TD_000043093022_003/runner", line 256, in run_lammps(infile, logfile) File "/disk2/worker/repository/td/ClusterEnergyAndForces__TD_000043093022_003/runner", line 56, in run_lammps raise Exception("LAMMPS did not exit properly:\n" + extrainfo) Exception: LAMMPS did not exit properly: LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task kim_init Sim_LAMMPS_Buckingham_CarreHorbachIspas_2008_SiO__SM_886641404623_000 metal unit_conversion_mode #=== BEGIN kim-init ========================================== # Using KIM Simulator Model : Sim_LAMMPS_Buckingham_CarreHorbachIspas_2008_SiO__SM_886641404623_000 # For Simulator : LAMMPS 29 Oct 2020 # Running on : LAMMPS 24 Dec 2020 # # Conversion factors from metal to metal: variable _u_mass internal 1.000000000000e+00 variable _u_distance internal 1.000000000000e+00 variable _u_time internal 1.000000000000e+00 variable _u_energy internal 1.000000000000e+00 variable _u_velocity internal 1.000000000000e+00 variable _u_force internal 1.000000000000e+00 variable _u_torque internal 1.000000000000e+00 variable _u_temperature internal 1.000000000000e+00 variable _u_pressure internal 1.000000000000e+00 variable _u_viscosity internal 1.000000000000e+00 variable _u_charge internal 1.000000000000e+00 variable _u_dipole internal 1.000000000000e+00 variable _u_efield internal 1.000000000000e+00 variable _u_density internal 1.000000000000e+00 # units metal atom_style charge neigh_modify one 4000 #=== END kim-init ============================================ boundary f f f variable boxextent equal 25.0 region box block -${boxextent} ${boxextent} -${boxextent} ${boxextent} -${boxextent} ${boxextent} region box block -25 ${boxextent} -${boxextent} ${boxextent} -${boxextent} ${boxextent} region box block -25 25 -${boxextent} ${boxextent} -${boxextent} ${boxextent} region box block -25 25 -25 ${boxextent} -${boxextent} ${boxextent} region box block -25 25 -25 25 -${boxextent} ${boxextent} region box block -25 25 -25 25 -25 ${boxextent} region box block -25 25 -25 25 -25 25 create_box 1 box Created orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) 1 by 1 by 1 MPI processor grid read_dump output/lammps_inputs/cluster.xyz 0 x y z box no add yes format xyz Scanning dump file ... Reading snapshot from dump file ... orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) 0 atoms before read 3 atoms in snapshot 0 atoms purged 0 atoms replaced 0 atoms trimmed 3 atoms added 3 atoms after read group all region box 3 atoms in group all variable mass1_converted equal 28.0855*${_u_mass} variable mass1_converted equal 28.0855*1 mass 1 ${mass1_converted} mass 1 28.0855 change_box all x scale ${_u_distance} y scale ${_u_distance} z scale ${_u_distance} remap change_box all x scale 1 y scale ${_u_distance} z scale ${_u_distance} remap change_box all x scale 1 y scale 1 z scale ${_u_distance} remap change_box all x scale 1 y scale 1 z scale 1 remap Changing box ... orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) atom_modify sort 0 0 kim_interactions Si #=== BEGIN kim_interactions ================================== variable kim_periodic equal 0 if "${kim_periodic} != 0" then "pair_style buck/coul/long 11.0" if "${kim_periodic} != 0" then "kspace_style pppm 1.0e-5" if "${kim_periodic} == 0" then "kspace_style none" kspace_style none if "${kim_periodic} == 2" then "kspace_modify slab 3.0" if "${kim_periodic} == 0" then "variable kim_cutoff equal ((lx+xy+xz)^2+(ly+yz)^2+(lz)^2)^(1/2)" variable kim_cutoff equal ((lx+xy+xz)^2+(ly+yz)^2+(lz)^2)^(1/2) if "${kim_periodic} == 0" then "pair_style buck/coul/cut 11.0 ${kim_cutoff}" pair_style buck/coul/cut 11.0 ${kim_cutoff} pair_style buck/coul/cut 11.0 86.6025403784439 set type 1 charge 1.910 Setting atom values ... 3 settings made for charge pair_coeff 1 1 3150.462646 0.3506986443 626.751953 #=== END kim_interactions ==================================== # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} nsq neighbor 2 nsq # Variables used to rescale the positions and forces so that the quantities in the # dumpfile are in the original metal units (angstrom and eV/angstrom) even if we're # running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable x_metal atom x/${_u_distance} variable x_metal atom x/1 variable y_metal atom y/${_u_distance} variable y_metal atom y/1 variable z_metal atom z/${_u_distance} variable z_metal atom z/1 variable fx_metal atom fx/${_u_force} variable fx_metal atom fx/1 variable fy_metal atom fy/${_u_force} variable fy_metal atom fy/1 variable fz_metal atom fz/${_u_force} variable fz_metal atom fz/1 dump dumpid all custom 1 output/lammps_dump/lammps.dump id type v_x_metal v_y_metal v_z_metal v_fx_metal v_fy_metal v_fz_metal dump_modify dumpid sort id format line "%d %d %16.7f %16.7f %16.7f %16.7f %16.7f %16.7f" thermo_style custom v_pe_metal # Define minimization (note that etol is actually unitless, but ftol has units of force) min_style cg variable dmax equal 0.1*${_u_distance} variable dmax equal 0.1*1 min_modify dmax ${dmax} min_modify dmax 0.1 variable ftol equal 1e-10*${_u_force} variable ftol equal 1e-10*1 minimize 1e-10 ${ftol} 2000 100000 minimize 1e-10 1e-10 2000 100000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 88.60254 ghost atom cutoff = 88.60254 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair buck/coul/cut, perpetual attributes: half, newton on pair build: half/nsq/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 6.155 | 6.155 | 6.155 Mbytes v_pe_metal 65.644166 ERROR: Lost atoms: original 3 current 1 (src/thermo.cpp:427) Last command: minimize 1e-10 ${ftol} 2000 100000 Command exited with non-zero status 1 {"usertime":0.40,"memmax":44668,"memavg":0}