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 = 3.5898365 3.5898365 3.5898365 Created orthogonal box = (0.0000000 -38.328965 0.0000000) to (22.129238 38.328965 6.2177792) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8234838 5.3795039 6.2177792 Created 455 atoms using lattice units in orthogonal box = (0.0000000 -38.328965 0.0000000) to (22.129238 38.328965 6.2177792) create_atoms CPU = 0.003 seconds 455 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8234838 5.3795039 6.2177792 Created 457 atoms using lattice units in orthogonal box = (0.0000000 -38.328965 0.0000000) to (22.129238 38.328965 6.2177792) create_atoms CPU = 0.002 seconds 457 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 21 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 912 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2835.5884 0 -2835.5884 82935.009 107 0 -3191.1211 0 -3191.1211 9509.3127 Loop time of 5.83073 on 1 procs for 107 steps with 912 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 = -2835.5883861897 -3191.1180092509 -3191.12106191386 Force two-norm initial, final = 574.65966 0.19500842 Force max component initial, final = 178.88049 0.034758026 Final line search alpha, max atom move = 1.0000000 0.034758026 Iterations, force evaluations = 107 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6802 | 5.6802 | 5.6802 | 0.0 | 97.42 Neigh | 0.10153 | 0.10153 | 0.10153 | 0.0 | 1.74 Comm | 0.024868 | 0.024868 | 0.024868 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02414 | | | 0.41 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5240.00 ave 5240 max 5240 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: 147866.0 ave 147866 max 147866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147866 Ave neighs/atom = 162.13377 Neighbor list builds = 5 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -3191.1211 0 -3191.1211 9509.3127 10547.726 113 0 -3191.387 0 -3191.387 -15.224211 10622.543 Loop time of 0.2674 on 1 procs for 6 steps with 912 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 = -3191.12106191386 -3191.3865454702 -3191.38701246378 Force two-norm initial, final = 112.90898 0.74643795 Force max component initial, final = 85.337833 0.62958165 Final line search alpha, max atom move = 0.00020778038 0.00013081471 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26265 | 0.26265 | 0.26265 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011202 | 0.0011202 | 0.0011202 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00363 | | | 1.36 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5271.00 ave 5271 max 5271 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: 149490.0 ave 149490 max 149490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149490 Ave neighs/atom = 163.91447 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.135 | 5.135 | 5.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3191.387 0 -3191.387 -15.224211 Loop time of 6.254e-06 on 1 procs for 0 steps with 912 atoms 175.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5243.00 ave 5243 max 5243 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: 142476.0 ave 142476 max 142476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142476 Ave neighs/atom = 156.22368 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.135 | 5.135 | 5.135 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 -3191.387 -3191.387 22.173922 77.012213 6.2205156 -15.224211 -15.224211 -95.150258 2.0723199 47.405305 2.3098055 644.75486 Loop time of 6.425e-06 on 1 procs for 0 steps with 912 atoms 264.6% 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 | | 6.425e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5243.00 ave 5243 max 5243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71238.0 ave 71238 max 71238 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142476.0 ave 142476 max 142476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142476 Ave neighs/atom = 156.22368 Neighbor list builds = 0 Dangerous builds = 0 912 -3191.38701246378 eV 2.30980552563644 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06