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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -40.621995 0.0000000) to (19.898852 40.621995 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3063606 4.8742035 5.9326915 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.621995 0.0000000) to (19.898852 40.621995 8.8990373) create_atoms CPU = 0.002 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3063606 4.8742035 5.9326915 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.621995 0.0000000) to (19.898852 40.621995 8.8990373) create_atoms CPU = 0.002 seconds 612 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 22 3 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 1188 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_036303866285_000#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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.454 | 5.454 | 5.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4999.1652 0 -4999.1652 12887.026 93 0 -5046.161 0 -5046.161 -7376.0402 Loop time of 3.09197 on 1 procs for 93 steps with 1188 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 = -4999.16515166777 -5046.15695284257 -5046.16101679646 Force two-norm initial, final = 41.564200 0.24431672 Force max component initial, final = 7.8891552 0.015440370 Final line search alpha, max atom move = 1.0000000 0.015440370 Iterations, force evaluations = 93 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0447 | 3.0447 | 3.0447 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023353 | 0.023353 | 0.023353 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02396 | | | 0.77 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5765.00 ave 5765 max 5765 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: 205320.0 ave 205320 max 205320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205320 Ave neighs/atom = 172.82828 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -5046.161 0 -5046.161 -7376.0402 14386.737 95 0 -5046.1948 0 -5046.1948 -4245.9008 14356.663 Loop time of 0.0670511 on 1 procs for 2 steps with 1188 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 = -5046.16101679645 -5046.19343133818 -5046.19475314234 Force two-norm initial, final = 45.457924 2.4537940 Force max component initial, final = 36.294377 2.4369338 Final line search alpha, max atom move = 0.00012790624 0.00031169904 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064923 | 0.064923 | 0.064923 | 0.0 | 96.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047862 | 0.00047862 | 0.00047862 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001649 | | | 2.46 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5691.00 ave 5691 max 5691 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: 181896.0 ave 181896 max 181896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181896 Ave neighs/atom = 153.11111 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.210 | 5.210 | 5.210 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5046.1948 0 -5046.1948 -4245.9008 Loop time of 6.234e-06 on 1 procs for 0 steps with 1188 atoms 176.5% 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 | | 6.234e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5699.00 ave 5699 max 5699 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: 189240.0 ave 189240 max 189240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189240 Ave neighs/atom = 159.29293 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.210 | 5.210 | 5.210 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 -5046.1948 -5046.1948 19.872248 81.243991 8.8923233 -4245.9008 -4245.9008 -0.84478359 -13008.61 271.75203 2.3296926 677.61022 Loop time of 6.586e-06 on 1 procs for 0 steps with 1188 atoms 273.3% 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 | | 6.586e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5699.00 ave 5699 max 5699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94620.0 ave 94620 max 94620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189240.0 ave 189240 max 189240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189240 Ave neighs/atom = 159.29293 Neighbor list builds = 0 Dangerous builds = 0 1188 -5046.19475314234 eV 2.32969263705753 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03