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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -39.064199 0.0000000) to (13.020196 39.064199 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0077677 5.0077677 3.6111526 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.064199 0.0000000) to (13.020196 39.064199 3.6111526) create_atoms CPU = 0.001 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0077677 5.0077677 3.6111526 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.064199 0.0000000) to (13.020196 39.064199 3.6111526) create_atoms CPU = 0.000 seconds 158 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 312 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1295.8255 0 -1295.8255 25688.526 57 0 -1319.2122 0 -1319.2122 7164.1499 Loop time of 1.62568 on 1 procs for 57 steps with 312 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1295.82550730096 -1319.21105895541 -1319.21218658915 Force two-norm initial, final = 34.088214 0.18219176 Force max component initial, final = 10.280506 0.062464885 Final line search alpha, max atom move = 1.0000000 0.062464885 Iterations, force evaluations = 57 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.622 | 1.622 | 1.622 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017212 | 0.0017212 | 0.0017212 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001935 | | | 0.12 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1928.00 ave 1928 max 1928 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: 16804.0 ave 16804 max 16804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16804 Ave neighs/atom = 53.858974 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.415 | 4.415 | 4.415 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -1319.2122 0 -1319.2122 7164.1499 3673.4344 63 0 -1319.2575 0 -1319.2575 1420.2895 3685.955 Loop time of 0.113778 on 1 procs for 6 steps with 312 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 = -1319.21218658915 -1319.25739376043 -1319.25745180004 Force two-norm initial, final = 20.892559 0.55218858 Force max component initial, final = 19.742059 0.44391755 Final line search alpha, max atom move = 0.0017956329 0.00079711295 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11312 | 0.11312 | 0.11312 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001223 | 0.0001223 | 0.0001223 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005389 | | | 0.47 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1966.00 ave 1966 max 1966 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: 16776.0 ave 16776 max 16776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16776 Ave neighs/atom = 53.769231 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1319.2575 0 -1319.2575 1420.2895 Loop time of 1.616e-06 on 1 procs for 0 steps with 312 atoms 123.8% 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 | | 1.616e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1966.00 ave 1966 max 1966 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: 16776.0 ave 16776 max 16776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16776 Ave neighs/atom = 53.769231 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.553 | 4.553 | 4.553 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 -1319.2575 -1319.2575 12.998837 78.128398 3.6294148 1420.2895 1420.2895 104.63328 3962.3015 193.93375 2.2592858 59.306909 Loop time of 1.324e-06 on 1 procs for 0 steps with 312 atoms 226.6% 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 | | 1.324e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1966.00 ave 1966 max 1966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8388.00 ave 8388 max 8388 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16776.0 ave 16776 max 16776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16776 Ave neighs/atom = 53.769231 Neighbor list builds = 0 Dangerous builds = 0 312 -1319.25745180004 eV 2.25928576662083 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01