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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -32.057539 0.0000000) to (16.028769 32.057539 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6989468 3.6989468 3.1435003 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -32.057539 0.0000000) to (16.028769 32.057539 3.1435003) create_atoms CPU = 0.001 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6989468 3.6989468 3.1435003 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -32.057539 0.0000000) to (16.028769 32.057539 3.1435003) create_atoms CPU = 0.000 seconds 106 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 13 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 208 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1307.1114 0 -1307.1114 95019.662 42 0 -1380.9188 0 -1380.9188 19384.104 Loop time of 0.214411 on 1 procs for 42 steps with 208 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 = -1307.11136415472 -1380.91746734445 -1380.91876133873 Force two-norm initial, final = 155.13618 0.19295679 Force max component initial, final = 54.647443 0.031444500 Final line search alpha, max atom move = 1.0000000 0.031444500 Iterations, force evaluations = 42 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21012 | 0.21012 | 0.21012 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029078 | 0.0029078 | 0.0029078 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001385 | | | 0.65 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4457.00 ave 4457 max 4457 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: 58340.0 ave 58340 max 58340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58340 Ave neighs/atom = 280.48077 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1380.9188 0 -1380.9188 19384.104 3230.5305 829 0 -1402.0461 0 -1402.0461 391.35346 3229.0957 Loop time of 2.83539 on 1 procs for 787 steps with 208 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1380.91876133873 -1402.04554470391 -1402.04610805398 Force two-norm initial, final = 113.63594 2.9048244 Force max component initial, final = 81.967527 2.1821380 Final line search alpha, max atom move = 0.00058078474 0.0012673525 Iterations, force evaluations = 787 1001 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6716 | 2.6716 | 2.6716 | 0.0 | 94.22 Neigh | 0.0066807 | 0.0066807 | 0.0066807 | 0.0 | 0.24 Comm | 0.031646 | 0.031646 | 0.031646 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1255 | | | 4.43 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4234.00 ave 4234 max 4234 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: 56840.0 ave 56840 max 56840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56840 Ave neighs/atom = 273.26923 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1402.0461 0 -1402.0461 391.35346 Loop time of 1.873e-06 on 1 procs for 0 steps with 208 atoms 106.8% 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 | | 1.873e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4793.00 ave 4793 max 4793 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: 57600.0 ave 57600 max 57600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57600 Ave neighs/atom = 276.92308 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.586 | 4.586 | 4.586 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 -1402.0461 -1402.0461 17.223035 66.525232 2.8182845 391.35346 391.35346 198.96373 4.4012004 970.69545 2.6382522 1205.1011 Loop time of 1.971e-06 on 1 procs for 0 steps with 208 atoms 253.7% 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 | | 1.971e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4793.00 ave 4793 max 4793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28800.0 ave 28800 max 28800 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57600.0 ave 57600 max 57600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57600 Ave neighs/atom = 276.92308 Neighbor list builds = 0 Dangerous builds = 0 208 -1402.04610805398 eV 2.63825221237007 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03