LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_BOP_ZhouWardFoster_2015_CuH__SM_404135993060_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.61954 3.61954 3.61954 Created orthogonal box = (0 -58.8142 0) to (20.7927 58.8142 5.11881) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.67073 4.45535 5.11881 Created 530 atoms create_atoms CPU = 0.000365019 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.67073 4.45535 5.11881 Created 530 atoms create_atoms CPU = 0.000207901 secs 530 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXaSQDNF/CuH.bop.table with DATE: 2015-07-06 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXaSQDNF/CuH.bop.table with DATE: 2015-07-06 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.9 ghost atom cutoff = 11.5 binsize = 3.45, bins = 7 35 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 1056 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.9 ghost atom cutoff = 11.5 binsize = 3.45, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.42 | 12.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3615.0927 0 -3615.0927 4333.0319 41 0 -3657.1067 0 -3657.1067 -2549.0636 Loop time of 7.38619 on 1 procs for 41 steps with 1056 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3615.09268319 -3657.10358474 -3657.10666968 Force two-norm initial, final = 29.0687 0.179748 Force max component initial, final = 6.63052 0.0240217 Final line search alpha, max atom move = 1 0.0240217 Iterations, force evaluations = 41 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3297 | 7.3297 | 7.3297 | 0.0 | 99.24 Neigh | 0.047937 | 0.047937 | 0.047937 | 0.0 | 0.65 Comm | 0.0063448 | 0.0063448 | 0.0063448 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002206 | | | 0.03 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12900 ave 12900 max 12900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139256 ave 139256 max 139256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139256 Ave neighs/atom = 131.871 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.42 | 12.42 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3657.1067 0 -3657.1067 -2549.0636 12519.643 43 0 -3657.1308 0 -3657.1308 101.84922 12496.094 Loop time of 0.389399 on 1 procs for 2 steps with 1056 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3657.10666968 -3657.12816177 -3657.13075015 Force two-norm initial, final = 31.6931 2.96419 Force max component initial, final = 29.4885 2.94149 Final line search alpha, max atom move = 0.000107765 0.000316991 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38844 | 0.38844 | 0.38844 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029874 | 0.00029874 | 0.00029874 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000658 | | | 0.17 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12876 ave 12876 max 12876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139240 ave 139240 max 139240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139240 Ave neighs/atom = 131.856 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.9 ghost atom cutoff = 11.5 binsize = 3.45, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 12.72 | 12.72 | 12.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3657.1308 0 -3657.1308 101.84922 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1056 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14241 ave 14241 max 14241 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139264 ave 139264 max 139264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139264 Ave neighs/atom = 131.879 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 12.72 | 12.72 | 12.72 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3657.1308 -3657.1308 20.785753 117.62847 5.1108844 101.84922 101.84922 377.01518 -111.85957 40.392045 2.3169639 402.02902 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1056 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14241 ave 14241 max 14241 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69632 ave 69632 max 69632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139264 ave 139264 max 139264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139264 Ave neighs/atom = 131.879 Neighbor list builds = 0 Dangerous builds = 0 1056 -3657.13075015134 eV 2.31696386725004 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08