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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -45.993613 0.0000000) to (32.519841 45.993613 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0221927 6.2455555 5.1100000 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.993613 0.0000000) to (32.519841 45.993613 5.1100000) create_atoms CPU = 0.005 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0221927 6.2455555 5.1100000 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.993613 0.0000000) to (32.519841 45.993613 5.1100000) create_atoms CPU = 0.004 seconds 650 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 33 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1288 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4516.0224 0 -4516.0224 7176.6585 56 0 -4548.7396 0 -4548.7396 -4425.7495 Loop time of 4.69099 on 1 procs for 56 steps with 1288 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 = -4516.02244965517 -4548.73515401869 -4548.73959485111 Force two-norm initial, final = 43.076200 0.18560012 Force max component initial, final = 11.892398 0.042956025 Final line search alpha, max atom move = 1.0000000 0.042956025 Iterations, force evaluations = 56 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6354 | 4.6354 | 4.6354 | 0.0 | 98.82 Neigh | 0.02711 | 0.02711 | 0.02711 | 0.0 | 0.58 Comm | 0.01326 | 0.01326 | 0.01326 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0152 | | | 0.32 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 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: 77008.0 ave 77008 max 77008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77008 Ave neighs/atom = 59.788820 Neighbor list builds = 2 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -4548.7396 0 -4548.7396 -4425.7495 15286.105 58 0 -4548.7693 0 -4548.7693 -1732.9792 15256.786 Loop time of 0.237745 on 1 procs for 2 steps with 1288 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4548.73959485111 -4548.7692857742 -4548.76930077739 Force two-norm initial, final = 43.621674 0.20398854 Force max component initial, final = 31.819511 0.052317510 Final line search alpha, max atom move = 0.0025212880 0.00013190751 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23515 | 0.23515 | 0.23515 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055993 | 0.00055993 | 0.00055993 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002037 | | | 0.86 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5044.00 ave 5044 max 5044 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: 77008.0 ave 77008 max 77008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77008 Ave neighs/atom = 59.788820 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.783 | 4.783 | 4.783 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4548.7693 0 -4548.7693 -1732.9792 Loop time of 6.194e-06 on 1 procs for 0 steps with 1288 atoms 193.7% 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 | | 6.194e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 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: 78312.0 ave 78312 max 78312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78312 Ave neighs/atom = 60.801242 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.783 | 4.783 | 4.783 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 -4548.7693 -4548.7693 32.486511 91.987226 5.1054315 -1732.9792 -1732.9792 4.9550944 -5198.4034 -5.4891604 2.3581545 516.8685 Loop time of 7.137e-06 on 1 procs for 0 steps with 1288 atoms 266.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39156.0 ave 39156 max 39156 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78312.0 ave 78312 max 78312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78312 Ave neighs/atom = 60.801242 Neighbor list builds = 0 Dangerous builds = 0 1288 -4548.76930077739 eV 2.35815453323719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05