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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.251551 0.0000000) to (20.623753 41.251551 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7593277 4.7593277 4.0446508 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.251551 0.0000000) to (20.623753 41.251551 4.0446508) create_atoms CPU = 0.001 seconds 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7593277 4.7593277 4.0446508 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.251551 0.0000000) to (20.623753 41.251551 4.0446508) create_atoms CPU = 0.001 seconds 209 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 25 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_127847080751_001#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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1368.4396 0 -1368.4396 5611.3546 46 0 -1378.2483 0 -1378.2483 -2216.6953 Loop time of 2.84019 on 1 procs for 46 steps with 412 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 = -1368.43961807593 -1378.24692451785 -1378.24828776036 Force two-norm initial, final = 12.318897 0.094198781 Force max component initial, final = 3.8677497 0.013238656 Final line search alpha, max atom move = 1.0000000 0.013238656 Iterations, force evaluations = 46 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8228 | 2.8228 | 2.8228 | 0.0 | 99.39 Neigh | 0.0052553 | 0.0052553 | 0.0052553 | 0.0 | 0.19 Comm | 0.0060555 | 0.0060555 | 0.0060555 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006046 | | | 0.21 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3116.00 ave 3116 max 3116 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: 31690.0 ave 31690 max 31690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31690 Ave neighs/atom = 76.917476 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1378.2483 0 -1378.2483 -2216.6953 6882.069 49 0 -1378.2749 0 -1378.2749 787.36014 6855.507 Loop time of 0.185936 on 1 procs for 3 steps with 412 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 = -1378.24828776036 -1378.27367528558 -1378.2748943862 Force two-norm initial, final = 19.148057 1.8980995 Force max component initial, final = 15.921518 1.8899955 Final line search alpha, max atom move = 0.00030458110 0.00057565691 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18444 | 0.18444 | 0.18444 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032893 | 0.00032893 | 0.00032893 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001167 | | | 0.63 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3132.00 ave 3132 max 3132 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: 31752.0 ave 31752 max 31752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31752 Ave neighs/atom = 77.067961 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1378.2749 0 -1378.2749 787.36014 Loop time of 6.394e-06 on 1 procs for 0 steps with 412 atoms 187.7% 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 | | 6.394e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3132.00 ave 3132 max 3132 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: 31772.0 ave 31772 max 31772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31772 Ave neighs/atom = 77.116505 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.582 | 4.582 | 4.582 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 -1378.2749 -1378.2749 20.60053 82.503103 4.0335821 787.36014 787.36014 441.20685 1887.8003 33.073291 2.6244099 273.62206 Loop time of 6.856e-06 on 1 procs for 0 steps with 412 atoms 248.0% 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 | | 6.856e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3132.00 ave 3132 max 3132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15886.0 ave 15886 max 15886 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31772.0 ave 31772 max 31772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31772 Ave neighs/atom = 77.116505 Neighbor list builds = 0 Dangerous builds = 0 412 -1378.2748943862 eV 2.6244098966984 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03