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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -52.207017 0.0000000) to (18.457968 52.207017 4.0766831) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9521377 4.4566965 4.0766831 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -52.207017 0.0000000) to (18.457968 52.207017 4.0766831) create_atoms CPU = 0.003 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9521377 4.4566965 4.0766831 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -52.207017 0.0000000) to (18.457968 52.207017 4.0766831) create_atoms CPU = 0.003 seconds 330 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 25 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 652 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2410.3543 0 -2410.3543 24772.34 113 0 -2517.5891 0 -2517.5891 -3044.2373 Loop time of 3.82214 on 1 procs for 113 steps with 652 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 = -2410.35426615952 -2517.58676098403 -2517.58907174167 Force two-norm initial, final = 213.35593 0.20003460 Force max component initial, final = 74.160100 0.036366954 Final line search alpha, max atom move = 1.0000000 0.036366954 Iterations, force evaluations = 113 207 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7329 | 3.7329 | 3.7329 | 0.0 | 97.67 Neigh | 0.03595 | 0.03595 | 0.03595 | 0.0 | 0.94 Comm | 0.031661 | 0.031661 | 0.031661 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0216 | | | 0.57 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6718.00 ave 6718 max 6718 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: 156504.0 ave 156504 max 156504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156504 Ave neighs/atom = 240.03681 Neighbor list builds = 2 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -2517.5891 0 -2517.5891 -3044.2373 7856.8725 118 0 -2517.7455 0 -2517.7455 21.824803 7842.2534 Loop time of 0.129427 on 1 procs for 5 steps with 652 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2517.58907174167 -2517.74499493862 -2517.74553859024 Force two-norm initial, final = 58.339366 0.57330641 Force max component initial, final = 41.669209 0.32019952 Final line search alpha, max atom move = 0.00045537103 0.00014580959 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1255 | 0.1255 | 0.1255 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095496 | 0.00095496 | 0.00095496 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002974 | | | 2.30 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6703.00 ave 6703 max 6703 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: 161004.0 ave 161004 max 161004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161004 Ave neighs/atom = 246.93865 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2517.7455 0 -2517.7455 21.824803 Loop time of 6.154e-06 on 1 procs for 0 steps with 652 atoms 195.0% 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 | | 6.154e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6713.00 ave 6713 max 6713 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: 160548.0 ave 160548 max 160548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160548 Ave neighs/atom = 246.23926 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.106 | 5.106 | 5.106 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 -2517.7455 -2517.7455 18.407204 104.82173 4.0644496 21.824803 21.824803 -45.225755 45.479538 65.220625 2.2875013 358.24736 Loop time of 7.297e-06 on 1 procs for 0 steps with 652 atoms 246.7% 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 | | 7.297e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6713.00 ave 6713 max 6713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80274.0 ave 80274 max 80274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160548.0 ave 160548 max 160548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160548 Ave neighs/atom = 246.23926 Neighbor list builds = 0 Dangerous builds = 0 652 -2517.74553859024 eV 2.28750126176009 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04