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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -32.091878 0.0000000) to (16.044366 32.091878 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7025459 3.7025459 3.1465590 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -32.091878 0.0000000) to (16.044366 32.091878 3.1465590) create_atoms CPU = 0.001 seconds 106 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7025459 3.7025459 3.1465590 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -32.091878 0.0000000) to (16.044366 32.091878 3.1465590) create_atoms CPU = 0.001 seconds 106 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 23 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 204 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.383 | 4.383 | 4.383 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1372.3226 0 -1372.3226 -32170.938 31 0 -1378.7901 0 -1378.7901 -34087.145 Loop time of 0.794234 on 1 procs for 31 steps with 204 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1372.32263309199 -1378.78887249802 -1378.79013989408 Force two-norm initial, final = 26.585817 0.11849901 Force max component initial, final = 11.758626 0.022385899 Final line search alpha, max atom move = 1.0000000 0.022385899 Iterations, force evaluations = 31 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78913 | 0.78913 | 0.78913 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028269 | 0.0028269 | 0.0028269 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002279 | | | 0.29 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1876.00 ave 1876 max 1876 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: 11544.0 ave 11544 max 11544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11544 Ave neighs/atom = 56.588235 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.382 | 4.382 | 4.382 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -1378.7901 0 -1378.7901 -34087.145 3240.2875 38 0 -1379.144 0 -1379.144 -6717.0764 3205.3566 Loop time of 0.11227 on 1 procs for 7 steps with 204 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1378.79013989408 -1379.14381199401 -1379.14397835689 Force two-norm initial, final = 91.402377 0.41838954 Force max component initial, final = 69.756304 0.29584734 Final line search alpha, max atom move = 0.00084621298 0.00025034986 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11064 | 0.11064 | 0.11064 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035682 | 0.00035682 | 0.00035682 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001276 | | | 1.14 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1831.00 ave 1831 max 1831 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: 11688.0 ave 11688 max 11688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11688 Ave neighs/atom = 57.294118 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1379.144 0 -1379.144 -6717.0764 Loop time of 6.434e-06 on 1 procs for 0 steps with 204 atoms 186.5% 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 | | 6.434e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1841.00 ave 1841 max 1841 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: 11704.0 ave 11704 max 11704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11704 Ave neighs/atom = 57.372549 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.520 | 4.520 | 4.520 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 -1379.144 -1379.144 15.970375 64.183755 3.1270593 -6717.0764 -6717.0764 147.1954 -20406.316 107.89168 2.4465543 126.14136 Loop time of 6.565e-06 on 1 procs for 0 steps with 204 atoms 243.7% 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 | | 6.565e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1841.00 ave 1841 max 1841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5852.00 ave 5852 max 5852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11704.0 ave 11704 max 11704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11704 Ave neighs/atom = 57.372549 Neighbor list builds = 0 Dangerous builds = 0 204 -1379.14397835689 eV 2.44655430304791 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01