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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -40.829228 0.0000000) to (14.435312 40.829228 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3182728 4.2978134 4.6834336 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -40.829228 0.0000000) to (14.435312 40.829228 4.6834336) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3182728 4.2978134 4.6834336 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -40.829228 0.0000000) to (14.435312 40.829228 4.6834336) create_atoms CPU = 0.001 seconds 306 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 4 22 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 610 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1923.4114 0 -1923.4114 259311.07 79 0 -2360.1598 0 -2360.1598 130913.92 Loop time of 1.0213 on 1 procs for 79 steps with 610 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1923.41139921917 -2360.15756824873 -2360.15984666458 Force two-norm initial, final = 399.01967 0.30470520 Force max component initial, final = 93.804476 0.063552113 Final line search alpha, max atom move = 1.0000000 0.063552113 Iterations, force evaluations = 79 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99719 | 0.99719 | 0.99719 | 0.0 | 97.64 Neigh | 0.0081802 | 0.0081802 | 0.0081802 | 0.0 | 0.80 Comm | 0.0099011 | 0.0099011 | 0.0099011 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00603 | | | 0.59 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5612.00 ave 5612 max 5612 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: 119560.0 ave 119560 max 119560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119560 Ave neighs/atom = 196.00000 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -2360.1598 0 -2360.1598 130913.92 5520.6689 584 0 -2458.9835 0 -2458.9835 -483.04092 6692.8981 Loop time of 3.25249 on 1 procs for 505 steps with 610 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2360.15984666459 -2458.98221231983 -2458.9834779679 Force two-norm initial, final = 810.16225 5.4790208 Force max component initial, final = 553.18689 3.2673151 Final line search alpha, max atom move = 0.00030689452 0.0010027211 Iterations, force evaluations = 505 541 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0392 | 3.0392 | 3.0392 | 0.0 | 93.44 Neigh | 0.069868 | 0.069868 | 0.069868 | 0.0 | 2.15 Comm | 0.025229 | 0.025229 | 0.025229 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1182 | | | 3.63 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4685.00 ave 4685 max 4685 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: 95716.0 ave 95716 max 95716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95716 Ave neighs/atom = 156.91148 Neighbor list builds = 10 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2458.9835 0 -2458.9835 -483.04092 Loop time of 1.761e-06 on 1 procs for 0 steps with 610 atoms 170.4% 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 | | 1.761e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4706.00 ave 4706 max 4706 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: 96940.0 ave 96940 max 96940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96940 Ave neighs/atom = 158.91803 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.692 | 4.692 | 4.692 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 -2458.9835 -2458.9835 15.765503 73.869505 5.7469999 -483.04092 -483.04092 -298.73523 -707.54031 -442.84721 2.2816738 812.28272 Loop time of 1.719e-06 on 1 procs for 0 steps with 610 atoms 174.5% 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 | | 1.719e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4706.00 ave 4706 max 4706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48470.0 ave 48470 max 48470 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96940.0 ave 96940 max 96940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96940 Ave neighs/atom = 158.91803 Neighbor list builds = 0 Dangerous builds = 0 610 -2458.98347796791 eV 2.28167380347957 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05