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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -74.678311 0.0000000) to (37.339156 74.678311 4.0500001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7106944 5.7106944 4.0500001 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.678311 0.0000000) to (37.339156 74.678311 4.0500001) create_atoms CPU = 0.001 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7106944 5.7106944 4.0500001 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.678311 0.0000000) to (37.339156 74.678311 4.0500001) create_atoms CPU = 0.001 seconds 682 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 40 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4519.5813 0 -4519.5813 11567.063 71 0 -4572.2967 0 -4572.2967 4034.1513 Loop time of 1.08337 on 1 procs for 71 steps with 1362 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4519.58125160591 -4572.2926918223 -4572.29667970147 Force two-norm initial, final = 53.878446 0.13545732 Force max component initial, final = 12.671447 0.035227976 Final line search alpha, max atom move = 1.0000000 0.035227976 Iterations, force evaluations = 71 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0519 | 1.0519 | 1.0519 | 0.0 | 97.09 Neigh | 0.010897 | 0.010897 | 0.010897 | 0.0 | 1.01 Comm | 0.010634 | 0.010634 | 0.010634 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009962 | | | 0.92 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8153.00 ave 8153 max 8153 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: 178312.0 ave 178312 max 178312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178312 Ave neighs/atom = 130.91924 Neighbor list builds = 1 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4572.2967 0 -4572.2967 4034.1513 22586.244 78 0 -4572.5941 0 -4572.5941 -96.142308 22704.004 Loop time of 0.0917301 on 1 procs for 7 steps with 1362 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 = -4572.29667970147 -4572.59130532161 -4572.59412718881 Force two-norm initial, final = 111.09075 2.4452368 Force max component initial, final = 98.787413 1.8599418 Final line search alpha, max atom move = 0.00016978218 0.00031578498 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076525 | 0.076525 | 0.076525 | 0.0 | 83.42 Neigh | 0.011054 | 0.011054 | 0.011054 | 0.0 | 12.05 Comm | 0.00086665 | 0.00086665 | 0.00086665 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003284 | | | 3.58 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8135.00 ave 8135 max 8135 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: 177720.0 ave 177720 max 177720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177720 Ave neighs/atom = 130.48458 Neighbor list builds = 1 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4572.5941 0 -4572.5941 -96.142308 Loop time of 2.203e-06 on 1 procs for 0 steps with 1362 atoms 181.6% 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 | | 2.203e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8135.00 ave 8135 max 8135 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: 177728.0 ave 177728 max 177728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177728 Ave neighs/atom = 130.49046 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.215 | 5.215 | 5.215 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 -4572.5941 -4572.5941 37.3173 150.3607 4.0462983 -96.142308 -96.142308 -70.21975 -87.074737 -131.13244 2.5740925 280.03251 Loop time of 2.403e-06 on 1 procs for 0 steps with 1362 atoms 249.7% 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 | | 2.403e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8135.00 ave 8135 max 8135 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88864.0 ave 88864 max 88864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 177728.0 ave 177728 max 177728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177728 Ave neighs/atom = 130.49046 Neighbor list builds = 0 Dangerous builds = 0 1362 -4572.59412718881 eV 2.57409251056443 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01