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 = 3.3901167 3.3901167 3.3901167 Created orthogonal box = (0.0000000 -41.520280 0.0000000) to (4.7943490 41.520280 5.8718543) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7943490 5.5360373 5.8718543 Created 60 atoms using lattice units in orthogonal box = (0.0000000 -41.520280 0.0000000) to (4.7943490 41.520280 5.8718543) create_atoms CPU = 0.001 seconds 60 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7943490 5.5360373 5.8718543 Created 62 atoms using lattice units in orthogonal box = (0.0000000 -41.520280 0.0000000) to (4.7943490 41.520280 5.8718543) create_atoms CPU = 0.000 seconds 62 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 1 9 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 120 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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 1 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4263.7335 0 -4263.7335 38376.759 213 0 -4377.1013 0 -4377.1013 -276395.77 Loop time of 1.2882 on 1 procs for 213 steps with 120 atoms 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4263.73348837524 -4377.0972136771 -4377.10129130852 Force two-norm initial, final = 47.859378 1.1141621 Force max component initial, final = 15.356825 0.19070881 Final line search alpha, max atom move = 0.12670920 0.024164561 Iterations, force evaluations = 213 406 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1791 | 1.1791 | 1.1791 | 0.0 | 91.53 Neigh | 0.042103 | 0.042103 | 0.042103 | 0.0 | 3.27 Comm | 0.052764 | 0.052764 | 0.052764 | 0.0 | 4.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01422 | | | 1.10 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13416.0 ave 13416 max 13416 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: 222794.0 ave 222794 max 222794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222794 Ave neighs/atom = 1856.6167 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 1 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 213 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 213 0 -4377.1013 0 -4377.1013 -276395.77 2337.7345 318 0 -4471.3044 0 -4471.3044 2519.8408 2280.6425 Loop time of 0.448671 on 1 procs for 105 steps with 120 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 = -4377.10129130851 -4471.30362097445 -4471.30435974 Force two-norm initial, final = 2442.0775 9.4320158 Force max component initial, final = 2313.8086 6.6727990 Final line search alpha, max atom move = 0.00027928696 0.0018636257 Iterations, force evaluations = 105 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35001 | 0.35001 | 0.35001 | 0.0 | 78.01 Neigh | 0.03581 | 0.03581 | 0.03581 | 0.0 | 7.98 Comm | 0.014286 | 0.014286 | 0.014286 | 0.0 | 3.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04856 | | | 10.82 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13704.0 ave 13704 max 13704 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: 227288.0 ave 227288 max 227288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227288 Ave neighs/atom = 1894.0667 Neighbor list builds = 4 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 1 8 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.629 | 5.629 | 5.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4471.3044 0 -4471.3044 2519.8408 Loop time of 2.235e-06 on 1 procs for 0 steps with 120 atoms 179.0% 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 | | 2.235e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13410.0 ave 13410 max 13410 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: 227360.0 ave 227360 max 227360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227360 Ave neighs/atom = 1894.6667 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 1 8 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.629 | 5.629 | 5.629 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 -4471.3044 -4471.3044 4.8916269 77.894955 5.9854191 2519.8408 2519.8408 2587.5953 4397.2408 574.68646 2.9856515 922.45613 Loop time of 2.536e-06 on 1 procs for 0 steps with 120 atoms 236.6% 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 | | 2.536e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13410.0 ave 13410 max 13410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113680.0 ave 113680 max 113680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227360.0 ave 227360 max 227360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227360 Ave neighs/atom = 1894.6667 Neighbor list builds = 0 Dangerous builds = 0 120 -4471.30435973999 eV 2.98565153370012 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01