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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -57.007818 0.0000000) to (34.910016 57.007818 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6306478 5.5168856 5.9114353 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -57.007818 0.0000000) to (34.910016 57.007818 8.8671530) create_atoms CPU = 0.002 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6306478 5.5168856 5.9114353 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -57.007818 0.0000000) to (34.910016 57.007818 8.8671530) create_atoms CPU = 0.002 seconds 1493 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2980 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.935 | 6.935 | 6.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10407.336 0 -10407.336 10378.53 51 0 -10523.718 0 -10523.718 6073.6217 Loop time of 2.44045 on 1 procs for 51 steps with 2980 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10407.3361565868 -10523.7080332638 -10523.7177823635 Force two-norm initial, final = 94.636293 0.33894885 Force max component initial, final = 18.150688 0.056728263 Final line search alpha, max atom move = 0.82925036 0.047041933 Iterations, force evaluations = 51 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.342 | 2.342 | 2.342 | 0.0 | 95.97 Neigh | 0.069083 | 0.069083 | 0.069083 | 0.0 | 2.83 Comm | 0.01296 | 0.01296 | 0.01296 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01639 | | | 0.67 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10479.0 ave 10479 max 10479 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: 519014.0 ave 519014 max 519014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519014 Ave neighs/atom = 174.16577 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.936 | 6.936 | 6.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -10523.718 0 -10523.718 6073.6217 35293.82 57 0 -10524.331 0 -10524.331 -304.57993 35461.178 Loop time of 0.220302 on 1 procs for 6 steps with 2980 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10523.7177823635 -10524.3268981633 -10524.3314853078 Force two-norm initial, final = 262.17306 12.817596 Force max component initial, final = 230.37536 9.0825472 Final line search alpha, max atom move = 5.7369600e-05 0.00052106210 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21451 | 0.21451 | 0.21451 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081699 | 0.00081699 | 0.00081699 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004973 | | | 2.26 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10485.0 ave 10485 max 10485 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: 519040.0 ave 519040 max 519040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519040 Ave neighs/atom = 174.17450 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.073 | 7.073 | 7.073 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10524.331 0 -10524.331 -304.57993 Loop time of 2.5e-06 on 1 procs for 0 steps with 2980 atoms 160.0% 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 | | 2.5e-06 | | |100.00 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10479.0 ave 10479 max 10479 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: 518368.0 ave 518368 max 518368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518368 Ave neighs/atom = 173.94899 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.073 | 7.073 | 7.073 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 -10524.331 -10524.331 34.920572 114.64348 8.8577305 -304.57993 -304.57993 -410.48393 -110.70349 -392.55237 2.3298097 1058.3772 Loop time of 2.785e-06 on 1 procs for 0 steps with 2980 atoms 323.2% 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 | | 2.785e-06 | | |100.00 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10479.0 ave 10479 max 10479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259184.0 ave 259184 max 259184 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 518368.0 ave 518368 max 518368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518368 Ave neighs/atom = 173.94899 Neighbor list builds = 0 Dangerous builds = 0 2980 -10524.3314853078 eV 2.32980966227417 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03