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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -35.897098 0.0000000) to (31.087799 35.897098 6.0968190) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5798613 5.5226305 6.0968190 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -35.897098 0.0000000) to (31.087799 35.897098 6.0968190) create_atoms CPU = 0.004 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5798613 5.5226305 6.0968190 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.897098 0.0000000) to (31.087799 35.897098 6.0968190) create_atoms CPU = 0.004 seconds 630 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 10 21 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1252 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_776437554506_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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 10 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5274.736 0 -5274.736 38718.574 71 0 -5539.6021 0 -5539.6021 18797.512 Loop time of 1.8867 on 1 procs for 71 steps with 1252 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 = -5274.73599493401 -5539.59689096887 -5539.60213504049 Force two-norm initial, final = 191.31407 0.26822515 Force max component initial, final = 39.890518 0.062009746 Final line search alpha, max atom move = 1.0000000 0.062009746 Iterations, force evaluations = 71 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7826 | 1.7826 | 1.7826 | 0.0 | 94.48 Neigh | 0.066956 | 0.066956 | 0.066956 | 0.0 | 3.55 Comm | 0.018308 | 0.018308 | 0.018308 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01888 | | | 1.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5877.00 ave 5877 max 5877 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: 165488.0 ave 165488 max 165488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165488 Ave neighs/atom = 132.17891 Neighbor list builds = 3 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 10 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -5539.6021 0 -5539.6021 18797.512 13607.634 82 0 -5541.0295 0 -5541.0295 -88.847592 13751.776 Loop time of 0.197801 on 1 procs for 11 steps with 1252 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 = -5539.6021350405 -5541.02930792382 -5541.02950722123 Force two-norm initial, final = 313.84615 1.6816343 Force max component initial, final = 273.13169 1.3492342 Final line search alpha, max atom move = 0.00039084670 0.00052734374 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18927 | 0.18927 | 0.18927 | 0.0 | 95.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016736 | 0.0016736 | 0.0016736 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006854 | | | 3.46 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5885.00 ave 5885 max 5885 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: 165572.0 ave 165572 max 165572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165572 Ave neighs/atom = 132.24601 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.186 | 5.186 | 5.186 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5541.0295 0 -5541.0295 -88.847592 Loop time of 6.004e-06 on 1 procs for 0 steps with 1252 atoms 166.6% 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 | | 6.004e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5877.00 ave 5877 max 5877 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: 165188.0 ave 165188 max 165188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165188 Ave neighs/atom = 131.93930 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.186 | 5.186 | 5.186 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 -5541.0295 -5541.0295 31.139944 72.516779 6.0897922 -88.847592 -88.847592 -157.45873 -84.868204 -24.215841 2.2504719 803.43287 Loop time of 6.415e-06 on 1 procs for 0 steps with 1252 atoms 296.2% 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 | | 6.415e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5877.00 ave 5877 max 5877 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82594.0 ave 82594 max 82594 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 165188.0 ave 165188 max 165188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165188 Ave neighs/atom = 131.93930 Neighbor list builds = 0 Dangerous builds = 0 1252 -5541.02950722125 eV 2.25047186130678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02