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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -35.683342 0.0000000) to (30.899651 35.683342 6.0599201) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5460912 5.4892067 6.0599201 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.683342 0.0000000) to (30.899651 35.683342 6.0599201) create_atoms CPU = 0.001 seconds 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5460912 5.4892067 6.0599201 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -35.683342 0.0000000) to (30.899651 35.683342 6.0599201) create_atoms CPU = 0.001 seconds 629 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 = 9 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 1226 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 = 9 19 2 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) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4966.4266 0 -4966.4266 16236.568 94 0 -5017.2969 0 -5017.2969 -14724.347 Loop time of 1.85704 on 1 procs for 94 steps with 1226 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 = -4966.42657299711 -5017.29325065944 -5017.29687404817 Force two-norm initial, final = 90.550544 0.28546029 Force max component initial, final = 30.970426 0.090081192 Final line search alpha, max atom move = 0.82203021 0.074049461 Iterations, force evaluations = 94 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8159 | 1.8159 | 1.8159 | 0.0 | 97.79 Neigh | 0.022971 | 0.022971 | 0.022971 | 0.0 | 1.24 Comm | 0.0092633 | 0.0092633 | 0.0092633 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00889 | | | 0.48 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6173.00 ave 6173 max 6173 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: 212328.0 ave 212328 max 212328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212328 Ave neighs/atom = 173.18760 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -5017.2969 0 -5017.2969 -14724.347 13363.37 99 0 -5017.573 0 -5017.573 -7021.1363 13275.112 Loop time of 0.0720628 on 1 procs for 5 steps with 1226 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 = -5017.29687404816 -5017.57173761499 -5017.57299937937 Force two-norm initial, final = 113.18347 1.3036233 Force max component initial, final = 93.190016 1.1304646 Final line search alpha, max atom move = 0.00014927674 0.00016875207 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07024 | 0.07024 | 0.07024 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033287 | 0.00033287 | 0.00033287 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00149 | | | 2.07 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6199.00 ave 6199 max 6199 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: 212424.0 ave 212424 max 212424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212424 Ave neighs/atom = 173.26591 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 = 9 19 2 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) = 5.589 | 5.589 | 5.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5017.573 0 -5017.573 -7021.1363 Loop time of 1.517e-06 on 1 procs for 0 steps with 1226 atoms 197.8% 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 | | 1.517e-06 | | |100.00 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6215.00 ave 6215 max 6215 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: 212714.0 ave 212714 max 212714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212714 Ave neighs/atom = 173.50245 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 = 9 19 2 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) = 5.589 | 5.589 | 5.589 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 -5017.573 -5017.573 30.764933 71.366685 6.0462584 -7021.1363 -7021.1363 28.213405 -21227.751 136.12846 2.2605821 985.97794 Loop time of 1.806e-06 on 1 procs for 0 steps with 1226 atoms 166.1% 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 | | 1.806e-06 | | |100.00 Nlocal: 1226.00 ave 1226 max 1226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6215.00 ave 6215 max 6215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106357.0 ave 106357 max 106357 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212714.0 ave 212714 max 212714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212714 Ave neighs/atom = 173.50245 Neighbor list builds = 0 Dangerous builds = 0 1226 -5017.57299937937 eV 2.26058212657809 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02