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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -40.902672 0.0000000) to (17.709811 40.902672 6.2613638) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9032704 5.1123821 6.2613638 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.902672 0.0000000) to (17.709811 40.902672 6.2613638) create_atoms CPU = 0.001 seconds 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9032704 5.1123821 6.2613638 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.902672 0.0000000) to (17.709811 40.902672 6.2613638) create_atoms CPU = 0.001 seconds 396 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 752 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2639.0246 0 -2639.0246 -6209.964 54 0 -2650.251 0 -2650.251 -23435.152 Loop time of 0.830574 on 1 procs for 54 steps with 752 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2639.02463242657 -2650.24850642969 -2650.25097492969 Force two-norm initial, final = 9.8883024 0.15179345 Force max component initial, final = 1.9363513 0.013919924 Final line search alpha, max atom move = 1.0000000 0.013919924 Iterations, force evaluations = 54 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82073 | 0.82073 | 0.82073 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0052592 | 0.0052592 | 0.0052592 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004588 | | | 0.55 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6292.00 ave 6292 max 6292 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: 165808.0 ave 165808 max 165808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165808 Ave neighs/atom = 220.48936 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2650.251 0 -2650.251 -23435.152 9071.196 64 0 -2650.8616 0 -2650.8616 -8893.504 8974.2358 Loop time of 0.102657 on 1 procs for 10 steps with 752 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 = -2650.2509749297 -2650.86102639267 -2650.86162646886 Force two-norm initial, final = 137.56340 1.4779940 Force max component initial, final = 119.95732 1.3684308 Final line search alpha, max atom move = 0.00030326721 0.00041500020 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099839 | 0.099839 | 0.099839 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005294 | 0.0005294 | 0.0005294 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002289 | | | 2.23 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5828.00 ave 5828 max 5828 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: 168400.0 ave 168400 max 168400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168400 Ave neighs/atom = 223.93617 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.142 | 5.142 | 5.142 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2650.8616 0 -2650.8616 -8893.504 Loop time of 1.743e-06 on 1 procs for 0 steps with 752 atoms 172.1% 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 | | 1.743e-06 | | |100.00 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5840.00 ave 5840 max 5840 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: 168768.0 ave 168768 max 168768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168768 Ave neighs/atom = 224.42553 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.142 | 5.142 | 5.142 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 -2650.8616 -2650.8616 17.548425 81.805344 6.2514054 -8893.504 -8893.504 -242.08057 -26349.127 -89.305024 2.4377067 416.76319 Loop time of 1.503e-06 on 1 procs for 0 steps with 752 atoms 199.6% 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 | | 1.503e-06 | | |100.00 Nlocal: 752.000 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5840.00 ave 5840 max 5840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84384.0 ave 84384 max 84384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168768.0 ave 168768 max 168768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168768 Ave neighs/atom = 224.42553 Neighbor list builds = 0 Dangerous builds = 0 752 -2650.86162646886 eV 2.43770665367866 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01