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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -48.543117 0.0000000) to (17.162584 48.543117 5.7208612) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7208612 6.7420996 5.7208612 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -48.543117 0.0000000) to (17.162584 48.543117 5.7208612) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7208612 6.7420996 5.7208612 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -48.543117 0.0000000) to (17.162584 48.543117 5.7208612) create_atoms CPU = 0.001 seconds 292 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 23 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 576 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_106969701023_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1932.68 0 -1932.68 13717.117 45 0 -1958.3729 0 -1958.3729 6566.9658 Loop time of 0.799048 on 1 procs for 45 steps with 576 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1932.67995571236 -1958.37096719104 -1958.37285908165 Force two-norm initial, final = 44.946653 0.093838148 Force max component initial, final = 8.4347669 0.010718827 Final line search alpha, max atom move = 1.0000000 0.010718827 Iterations, force evaluations = 45 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78927 | 0.78927 | 0.78927 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057555 | 0.0057555 | 0.0057555 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004019 | | | 0.50 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4760.00 ave 4760 max 4760 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: 81424.0 ave 81424 max 81424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81424 Ave neighs/atom = 141.36111 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -1958.3729 0 -1958.3729 6566.9658 9532.3887 56 0 -1958.7215 0 -1958.7215 -16.330548 9606.7662 Loop time of 0.152357 on 1 procs for 11 steps with 576 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1958.37285908165 -1958.7199090814 -1958.72149314814 Force two-norm initial, final = 79.340630 0.40169079 Force max component initial, final = 72.874725 0.25928507 Final line search alpha, max atom move = 0.00035977618 9.3284592e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13548 | 0.13548 | 0.13548 | 0.0 | 88.92 Neigh | 0.010385 | 0.010385 | 0.010385 | 0.0 | 6.82 Comm | 0.0016367 | 0.0016367 | 0.0016367 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004854 | | | 3.19 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4768.00 ave 4768 max 4768 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: 80752.0 ave 80752 max 80752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80752 Ave neighs/atom = 140.19444 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.673 | 4.673 | 4.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1958.7215 0 -1958.7215 -16.330548 Loop time of 3.032e-06 on 1 procs for 0 steps with 576 atoms 164.9% 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 | | 3.032e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4768.00 ave 4768 max 4768 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: 80768.0 ave 80768 max 80768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80768 Ave neighs/atom = 140.22222 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.673 | 4.673 | 4.673 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 -1958.7215 -1958.7215 17.127553 98.129264 5.7158833 -16.330548 -16.330548 -43.154223 -27.191733 21.354312 2.6780527 401.15221 Loop time of 2.92e-06 on 1 procs for 0 steps with 576 atoms 171.2% 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 | | 2.92e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4768.00 ave 4768 max 4768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40384.0 ave 40384 max 40384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80768.0 ave 80768 max 80768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80768 Ave neighs/atom = 140.22222 Neighbor list builds = 0 Dangerous builds = 0 576 -1958.72149314814 eV 2.6780526703201 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01