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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -25.086938 0.0000000) to (21.725926 25.086938 4.2608046) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8995252 3.8595290 4.2608046 Created 309 atoms using lattice units in orthogonal box = (0.0000000 -25.086938 0.0000000) to (21.725926 25.086938 4.2608046) create_atoms CPU = 0.001 seconds 309 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8995252 3.8595290 4.2608046 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -25.086938 0.0000000) to (21.725926 25.086938 4.2608046) create_atoms CPU = 0.001 seconds 316 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 14 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 625 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_677328661525_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6496.2156 0 -6496.2156 889746.96 368 0 -7907.0389 0 -7907.0389 251370.11 Loop time of 27.7502 on 1 procs for 368 steps with 625 atoms 96.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6496.21557426341 -7907.03117551459 -7907.03890856854 Force two-norm initial, final = 4519.8999 0.87646669 Force max component initial, final = 1420.4954 0.39854705 Final line search alpha, max atom move = 0.29230169 0.11649598 Iterations, force evaluations = 368 726 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.628 | 27.628 | 27.628 | 0.0 | 99.56 Neigh | 0.061958 | 0.061958 | 0.061958 | 0.0 | 0.22 Comm | 0.035746 | 0.035746 | 0.035746 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02447 | | | 0.09 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5670.00 ave 5670 max 5670 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: 152934.0 ave 152934 max 152934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152934 Ave neighs/atom = 244.69440 Neighbor list builds = 7 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 368 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.930 | 4.930 | 4.930 Mbytes Step Temp E_pair E_mol TotEng Press Volume 368 0 -7907.0389 0 -7907.0389 251370.11 4644.592 416 0 -7943.0424 0 -7943.0424 -2057.6641 4798.3768 Loop time of 1.82325 on 1 procs for 48 steps with 625 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 = -7907.03890856856 -7943.03495975321 -7943.04241784499 Force two-norm initial, final = 1737.9033 13.996583 Force max component initial, final = 1511.1352 7.7771914 Final line search alpha, max atom move = 7.2006430e-05 0.00056000779 Iterations, force evaluations = 48 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8019 | 1.8019 | 1.8019 | 0.0 | 98.83 Neigh | 0.0086324 | 0.0086324 | 0.0086324 | 0.0 | 0.47 Comm | 0.0023605 | 0.0023605 | 0.0023605 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0104 | | | 0.57 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5398.00 ave 5398 max 5398 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: 148268.0 ave 148268 max 148268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148268 Ave neighs/atom = 237.22880 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7943.0424 0 -7943.0424 -2057.6641 Loop time of 1.889e-06 on 1 procs for 0 steps with 625 atoms 158.8% 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 | | 1.889e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5394.00 ave 5394 max 5394 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: 148192.0 ave 148192 max 148192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148192 Ave neighs/atom = 237.10720 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.066 | 5.066 | 5.066 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 -7943.0424 -7943.0424 22.082961 49.119304 4.4236916 -2057.6641 -2057.6641 -1745.2149 -1731.702 -2696.0753 1.8895307 2683.7716 Loop time of 2.714e-06 on 1 procs for 0 steps with 625 atoms 405.3% 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 | | 2.714e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5394.00 ave 5394 max 5394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74096.0 ave 74096 max 74096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 148192.0 ave 148192 max 148192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148192 Ave neighs/atom = 237.10720 Neighbor list builds = 0 Dangerous builds = 0 625 -7943.04241784499 eV 1.88953066224558 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29