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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -56.929079 0.0000000) to (34.861799 56.929079 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6228708 5.5092658 5.9032705 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -56.929079 0.0000000) to (34.861799 56.929079 8.8549058) create_atoms CPU = 0.006 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6228708 5.5092658 5.9032705 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -56.929079 0.0000000) to (34.861799 56.929079 8.8549058) create_atoms CPU = 0.006 seconds 1493 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 30 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2976 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.905 | 6.905 | 6.905 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10201.633 0 -10201.633 10952.459 68 0 -10508.722 0 -10508.722 3501.5742 Loop time of 5.38837 on 1 procs for 68 steps with 2976 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10201.6328908981 -10508.7129397128 -10508.7219693419 Force two-norm initial, final = 94.850257 0.27717064 Force max component initial, final = 8.4592977 0.026570097 Final line search alpha, max atom move = 1.0000000 0.026570097 Iterations, force evaluations = 68 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2562 | 5.2562 | 5.2562 | 0.0 | 97.55 Neigh | 0.066995 | 0.066995 | 0.066995 | 0.0 | 1.24 Comm | 0.029085 | 0.029085 | 0.029085 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03612 | | | 0.67 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10185.0 ave 10185 max 10185 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: 506526.0 ave 506526 max 506526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506526 Ave neighs/atom = 170.20363 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.908 | 6.908 | 6.908 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -10508.722 0 -10508.722 3501.5742 35147.78 71 0 -10508.873 0 -10508.873 -1.0172014 35236.875 Loop time of 0.2803 on 1 procs for 3 steps with 2976 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 = -10508.7219693419 -10508.8648225065 -10508.8731215369 Force two-norm initial, final = 144.14621 0.52985976 Force max component initial, final = 114.14829 0.37801218 Final line search alpha, max atom move = 3.0988208e-05 1.1713920e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27296 | 0.27296 | 0.27296 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014647 | 0.0014647 | 0.0014647 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005878 | | | 2.10 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10405.0 ave 10405 max 10405 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: 506286.0 ave 506286 max 506286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506286 Ave neighs/atom = 170.12298 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.045 | 7.045 | 7.045 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10508.873 0 -10508.873 -1.0172014 Loop time of 6.465e-06 on 1 procs for 0 steps with 2976 atoms 185.6% 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 | | 6.465e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10394.0 ave 10394 max 10394 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: 502012.0 ave 502012 max 502012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502012 Ave neighs/atom = 168.68683 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.045 | 7.045 | 7.045 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 -10508.873 -10508.873 34.937307 113.96786 8.8496389 -1.0172014 -1.0172014 8.686052 -17.2043 5.4666441 2.3238642 947.22295 Loop time of 7.437e-06 on 1 procs for 0 steps with 2976 atoms 268.9% 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 | | 7.437e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10394.0 ave 10394 max 10394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251006.0 ave 251006 max 251006 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 502012.0 ave 502012 max 502012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502012 Ave neighs/atom = 168.68683 Neighbor list builds = 0 Dangerous builds = 0 2976 -10508.8731215369 eV 2.32386416292182 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06