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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -45.189370 0.0000000) to (15.063123 45.189370 3.6533440) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4303304 4.4303304 3.6533440 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -45.189370 0.0000000) to (15.063123 45.189370 3.6533440) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4303304 4.4303304 3.6533440 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -45.189370 0.0000000) to (15.063123 45.189370 3.6533440) create_atoms CPU = 0.001 seconds 206 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 1 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1280.903 0 -1280.903 24067.436 53 0 -1325.7444 0 -1325.7444 4642.3782 Loop time of 1.01486 on 1 procs for 53 steps with 408 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 = -1280.90297543793 -1325.74335340317 -1325.74436552009 Force two-norm initial, final = 96.729239 0.11559778 Force max component initial, final = 30.668751 0.018306730 Final line search alpha, max atom move = 1.0000000 0.018306730 Iterations, force evaluations = 53 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98184 | 0.98184 | 0.98184 | 0.0 | 96.75 Neigh | 0.012098 | 0.012098 | 0.012098 | 0.0 | 1.19 Comm | 0.013179 | 0.013179 | 0.013179 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007737 | | | 0.76 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5384.00 ave 5384 max 5384 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: 91252.0 ave 91252 max 91252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91252 Ave neighs/atom = 223.65686 Neighbor list builds = 1 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1325.7444 0 -1325.7444 4642.3782 4973.6119 58 0 -1325.7908 0 -1325.7908 -5.0820936 4991.3431 Loop time of 0.0825083 on 1 procs for 5 steps with 408 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1325.7443655201 -1325.79072100748 -1325.7908332136 Force two-norm initial, final = 27.186859 0.19100868 Force max component initial, final = 22.005180 0.067042059 Final line search alpha, max atom move = 0.00065012103 4.3585452e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07873 | 0.07873 | 0.07873 | 0.0 | 95.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091262 | 0.00091262 | 0.00091262 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002865 | | | 3.47 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5339.00 ave 5339 max 5339 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: 91176.0 ave 91176 max 91176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91176 Ave neighs/atom = 223.47059 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 4.649 | 4.649 | 4.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1325.7908 0 -1325.7908 -5.0820936 Loop time of 6.314e-06 on 1 procs for 0 steps with 408 atoms 190.1% 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 | | 6.314e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5349.00 ave 5349 max 5349 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: 91112.0 ave 91112 max 91112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91112 Ave neighs/atom = 223.31373 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 4.649 | 4.649 | 4.649 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 -1325.7908 -1325.7908 15.040809 90.727282 3.6577021 -5.0820936 -5.0820936 5.4702158 0.82907565 -21.545572 2.3087652 203.31715 Loop time of 6.595e-06 on 1 procs for 0 steps with 408 atoms 257.8% 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 | | 6.595e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5349.00 ave 5349 max 5349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45556.0 ave 45556 max 45556 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91112.0 ave 91112 max 91112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91112 Ave neighs/atom = 223.31373 Neighbor list builds = 0 Dangerous builds = 0 408 -1325.7908332136 eV 2.30876516867522 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01