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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -66.979512 0.0000000) to (23.679557 66.979512 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0575611 6.2303164 5.1068646 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.979512 0.0000000) to (23.679557 66.979512 5.1068646) create_atoms CPU = 0.002 seconds 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0575611 6.2303164 5.1068646 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.979512 0.0000000) to (23.679557 66.979512 5.1068646) create_atoms CPU = 0.002 seconds 690 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 ghost atom cutoff = 6 binsize = 3, bins = 8 45 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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_150993986463_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5763.6233 0 -5763.6233 2115.3278 138 0 -5796.1652 0 -5796.1652 -7409.2481 Loop time of 23.0491 on 1 procs for 138 steps with 1368 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 = -5763.62334788741 -5796.15950379622 -5796.1651921332 Force two-norm initial, final = 38.101768 0.23464258 Force max component initial, final = 11.280247 0.055263918 Final line search alpha, max atom move = 0.94720371 0.052346188 Iterations, force evaluations = 138 260 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.941 | 22.941 | 22.941 | 0.0 | 99.53 Neigh | 0.047181 | 0.047181 | 0.047181 | 0.0 | 0.20 Comm | 0.030852 | 0.030852 | 0.030852 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03008 | | | 0.13 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5918.00 ave 5918 max 5918 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: 105720.0 ave 105720 max 105720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105720 Ave neighs/atom = 77.280702 Neighbor list builds = 3 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 ghost atom cutoff = 6 binsize = 3, bins = 8 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 138 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 138 0 -5796.1652 0 -5796.1652 -7409.2481 16199.436 140 0 -5796.2139 0 -5796.2139 -3643.0789 16163.57 Loop time of 0.355469 on 1 procs for 2 steps with 1368 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 = -5796.1651921332 -5796.21131493333 -5796.21393868639 Force two-norm initial, final = 61.674634 4.2931705 Force max component initial, final = 49.777139 4.0958612 Final line search alpha, max atom move = 7.7541395e-05 0.00031759879 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35349 | 0.35349 | 0.35349 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037164 | 0.00037164 | 0.00037164 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001611 | | | 0.45 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5916.00 ave 5916 max 5916 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: 105892.0 ave 105892 max 105892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105892 Ave neighs/atom = 77.406433 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 ghost atom cutoff = 6 binsize = 3, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5796.2139 0 -5796.2139 -3643.0789 Loop time of 3.236e-06 on 1 procs for 0 steps with 1368 atoms 154.5% 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 | | 3.236e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5922.00 ave 5922 max 5922 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: 105928.0 ave 105928 max 105928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105928 Ave neighs/atom = 77.432749 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 ghost atom cutoff = 6 binsize = 3, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.213 | 5.213 | 5.213 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 -5796.2139 -5796.2139 23.647071 133.95902 5.102558 -3643.0789 -3643.0789 -125.11114 -11209.776 405.6504 2.3657215 610.67712 Loop time of 3.541e-06 on 1 procs for 0 steps with 1368 atoms 169.4% 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 | | 3.541e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5922.00 ave 5922 max 5922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52964.0 ave 52964 max 52964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105928.0 ave 105928 max 105928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105928 Ave neighs/atom = 77.432749 Neighbor list builds = 0 Dangerous builds = 0 1368 -5796.21393868639 eV 2.36572149781116 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24