LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -43.111019 0.0000000) to (4.9780317 43.111019 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9780317 5.7481359 6.0968188 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.111019 0.0000000) to (4.9780317 43.111019 6.0968188) create_atoms CPU = 0.003 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9780317 5.7481359 6.0968188 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.111019 0.0000000) to (4.9780317 43.111019 6.0968188) create_atoms CPU = 0.003 seconds 122 atoms in group lower Displacing atoms ... 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_800536961967_003#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1068 0 -1068 0.018019259 1 0 -1068 0 -1068 0.018019259 Loop time of 0.0216739 on 1 procs for 1 steps with 240 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1068.00000000008 -1068.00000000008 -1068.00000000006 Force two-norm initial, final = 1.2619625e-07 4.4264318e-08 Force max component initial, final = 3.9093415e-08 1.4499715e-08 Final line search alpha, max atom move = 1.0000000 1.4499715e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020693 | 0.020693 | 0.020693 | 0.0 | 95.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004901 | 0.0004901 | 0.0004901 | 0.0 | 2.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004911 | | | 2.27 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3242.00 ave 3242 max 3242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32160.0 ave 32160 max 32160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32160 Ave neighs/atom = 134.00000 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -1068 0 -1068 0.018019259 2616.8525 2 0 -1068 0 -1068 -2.8713768e-06 2616.8525 Loop time of 0.0159042 on 1 procs for 1 steps with 240 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1068.00000000005 -1068.00000000005 -1068.0000000001 Force two-norm initial, final = 5.0976629e-05 1.4659230e-07 Force max component initial, final = 2.9542154e-05 1.1856974e-07 Final line search alpha, max atom move = 1.0000000 1.1856974e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.014694 | 0.014694 | 0.014694 | 0.0 | 92.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032052 | 0.00032052 | 0.00032052 | 0.0 | 2.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008895 | | | 5.59 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3242.00 ave 3242 max 3242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32160.0 ave 32160 max 32160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32160 Ave neighs/atom = 134.00000 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1068 0 -1068 -2.8713782e-06 Loop time of 1.1487e-05 on 1 procs for 0 steps with 240 atoms 139.3% 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 | | 1.149e-05 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3242.00 ave 3242 max 3242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32160.0 ave 32160 max 32160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32160 Ave neighs/atom = 134.00000 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.625 | 4.625 | 4.625 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 -1068 -1068 4.9780317 86.222039 6.0968188 -2.8713782e-06 -2.8713782e-06 3.0259695e-05 -7.2594723e-05 3.3720893e-05 2.4890159 3.4181761e-16 Loop time of 1.3943e-05 on 1 procs for 0 steps with 240 atoms 193.6% 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 | | 1.394e-05 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3242.00 ave 3242 max 3242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16080.0 ave 16080 max 16080 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32160.0 ave 32160 max 32160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32160 Ave neighs/atom = 134.00000 Neighbor list builds = 0 Dangerous builds = 0 240 -1068.0000000001 eV 2.48901586946566 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00