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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -50.170751 0.0000000) to (35.473308 50.170751 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0564185 6.7296972 5.5400000 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -50.170751 0.0000000) to (35.473308 50.170751 5.5400000) create_atoms CPU = 0.005 seconds 660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0564185 6.7296972 5.5400000 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -50.170751 0.0000000) to (35.473308 50.170751 5.5400000) create_atoms CPU = 0.005 seconds 660 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1296 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.040 | 5.040 | 5.040 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7418.758 0 -7418.758 32.727519 38 0 -7447.2372 0 -7447.2372 -11892.343 Loop time of 3.54032 on 1 procs for 38 steps with 1296 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 = -7418.75798682962 -7447.23081939172 -7447.23718960883 Force two-norm initial, final = 36.559006 0.28986856 Force max component initial, final = 8.4856216 0.052732747 Final line search alpha, max atom move = 1.0000000 0.052732747 Iterations, force evaluations = 38 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.519 | 3.519 | 3.519 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010319 | 0.010319 | 0.010319 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01096 | | | 0.31 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5697.00 ave 5697 max 5697 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: 99600.0 ave 99600 max 99600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99600 Ave neighs/atom = 76.851852 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.040 | 5.040 | 5.040 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -7447.2372 0 -7447.2372 -11892.343 19719.326 41 0 -7447.3534 0 -7447.3534 -6875.2699 19661.866 Loop time of 0.295757 on 1 procs for 3 steps with 1296 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 = -7447.23718960883 -7447.35238152771 -7447.35342352276 Force two-norm initial, final = 109.31577 0.32833943 Force max component initial, final = 85.212363 0.070483048 Final line search alpha, max atom move = 0.00018510990 1.3047110e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29224 | 0.29224 | 0.29224 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076811 | 0.00076811 | 0.00076811 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002753 | | | 0.93 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5669.00 ave 5669 max 5669 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: 100088.0 ave 100088 max 100088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100088 Ave neighs/atom = 77.228395 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.178 | 5.178 | 5.178 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7447.3534 0 -7447.3534 -6875.2699 Loop time of 6.264e-06 on 1 procs for 0 steps with 1296 atoms 191.6% 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 | | 6.264e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5669.00 ave 5669 max 5669 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: 100096.0 ave 100096 max 100096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100096 Ave neighs/atom = 77.234568 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.178 | 5.178 | 5.178 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 -7447.3534 -7447.3534 35.405452 100.3415 5.534444 -6875.2699 -6875.2699 -1.0146041 -20619.057 -5.7376563 2.5947751 758.41465 Loop time of 7.207e-06 on 1 procs for 0 steps with 1296 atoms 277.5% 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 | | 7.207e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5669.00 ave 5669 max 5669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50048.0 ave 50048 max 50048 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100096.0 ave 100096 max 100096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100096 Ave neighs/atom = 77.234568 Neighbor list builds = 0 Dangerous builds = 0 1296 -7447.35342352276 eV 2.59477512339203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04