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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -39.414105 0.0000000) to (10.726380 39.414105 7.0220643) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5970202 4.3790265 4.6813762 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.414105 0.0000000) to (10.726380 39.414105 7.0220643) create_atoms CPU = 0.002 seconds 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5970202 4.3790265 4.6813762 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.414105 0.0000000) to (10.726380 39.414105 7.0220643) create_atoms CPU = 0.001 seconds 254 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 3 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 500 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2070.8379 0 -2070.8379 33337.511 117 0 -2125.2826 0 -2125.2826 -7287.4726 Loop time of 1.90014 on 1 procs for 117 steps with 500 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 = -2070.8378562034 -2125.28094221611 -2125.28263963885 Force two-norm initial, final = 110.96640 0.18927662 Force max component initial, final = 42.541319 0.042910234 Final line search alpha, max atom move = 1.0000000 0.042910234 Iterations, force evaluations = 117 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8365 | 1.8365 | 1.8365 | 0.0 | 96.65 Neigh | 0.02498 | 0.02498 | 0.02498 | 0.0 | 1.31 Comm | 0.021835 | 0.021835 | 0.021835 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01682 | | | 0.88 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4146.00 ave 4146 max 4146 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: 83072.0 ave 83072 max 83072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83072 Ave neighs/atom = 166.14400 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -2125.2826 0 -2125.2826 -7287.4726 5937.4459 120 0 -2125.3231 0 -2125.3231 -1431.1887 5921.3084 Loop time of 0.0520324 on 1 procs for 3 steps with 500 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 = -2125.28263963885 -2125.32266803052 -2125.32305471728 Force two-norm initial, final = 38.170770 0.23330623 Force max component initial, final = 33.363902 0.044993976 Final line search alpha, max atom move = 0.00037731291 1.6976808e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049824 | 0.049824 | 0.049824 | 0.0 | 95.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056063 | 0.00056063 | 0.00056063 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001648 | | | 3.17 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4089.00 ave 4089 max 4089 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: 83032.0 ave 83032 max 83032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83032 Ave neighs/atom = 166.06400 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2125.3231 0 -2125.3231 -1431.1887 Loop time of 6.435e-06 on 1 procs for 0 steps with 500 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4092.00 ave 4092 max 4092 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: 83072.0 ave 83072 max 83072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83072 Ave neighs/atom = 166.14400 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.683 | 4.683 | 4.683 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 -2125.3231 -2125.3231 10.719136 78.82821 7.0077121 -1431.1887 -1431.1887 -5.3819874 -4291.5789 3.3947711 2.3045468 432.56624 Loop time of 7.076e-06 on 1 procs for 0 steps with 500 atoms 268.5% 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 | | 7.076e-06 | | |100.00 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4092.00 ave 4092 max 4092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41536.0 ave 41536 max 41536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83072.0 ave 83072 max 83072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83072 Ave neighs/atom = 166.14400 Neighbor list builds = 0 Dangerous builds = 0 500 -2125.32305471728 eV 2.30454678310784 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02