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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -60.141249 0.0000000) to (30.068865 60.141249 3.5192945) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5309249 4.5309249 3.5192945 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -60.141249 0.0000000) to (30.068865 60.141249 3.5192945) create_atoms CPU = 0.001 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5309249 4.5309249 3.5192945 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -60.141249 0.0000000) to (30.068865 60.141249 3.5192945) create_atoms CPU = 0.001 seconds 586 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1156 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.460 | 5.460 | 5.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5112.2068 0 -5112.2068 1706.103 61 0 -5125.6233 0 -5125.6233 -7865.3412 Loop time of 1.23682 on 1 procs for 61 steps with 1156 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 = -5112.2067540948 -5125.61866868951 -5125.62328580511 Force two-norm initial, final = 34.998714 0.23814589 Force max component initial, final = 10.463770 0.018476906 Final line search alpha, max atom move = 1.0000000 0.018476906 Iterations, force evaluations = 61 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.221 | 1.221 | 1.221 | 0.0 | 98.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0089834 | 0.0089834 | 0.0089834 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006827 | | | 0.55 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9532.00 ave 9532 max 9532 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: 200980.0 ave 200980 max 200980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200980 Ave neighs/atom = 173.85813 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.460 | 5.460 | 5.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -5125.6233 0 -5125.6233 -7865.3412 12728.437 64 0 -5125.7592 0 -5125.7592 -398.38737 12674.758 Loop time of 0.053171 on 1 procs for 3 steps with 1156 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 = -5125.62328580511 -5125.75727028947 -5125.75916247761 Force two-norm initial, final = 92.587222 4.3976166 Force max component initial, final = 67.862513 4.3000456 Final line search alpha, max atom move = 0.00010749821 0.00046224719 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051462 | 0.051462 | 0.051462 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001353 | | | 2.55 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9586.00 ave 9586 max 9586 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: 201112.0 ave 201112 max 201112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201112 Ave neighs/atom = 173.97232 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.598 | 5.598 | 5.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5125.7592 0 -5125.7592 -398.38737 Loop time of 1.84e-06 on 1 procs for 0 steps with 1156 atoms 163.0% 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 | | 1.84e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9603.00 ave 9603 max 9603 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: 201176.0 ave 201176 max 201176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201176 Ave neighs/atom = 174.02768 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.598 | 5.598 | 5.598 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 -5125.7592 -5125.7592 30.013785 120.2825 3.510884 -398.38737 -398.38737 542.55961 -1626.6773 -111.0444 2.1970131 504.98907 Loop time of 2.202e-06 on 1 procs for 0 steps with 1156 atoms 181.7% 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 | | 2.202e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9603.00 ave 9603 max 9603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100588.0 ave 100588 max 100588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201176.0 ave 201176 max 201176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201176 Ave neighs/atom = 174.02768 Neighbor list builds = 0 Dangerous builds = 0 1156 -5125.75916247761 eV 2.19701306369767 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01