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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -56.552248 0.0000000) to (28.276124 56.552248 3.6203867) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0989732 5.0989732 3.6203867 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.552248 0.0000000) to (28.276124 56.552248 3.6203867) create_atoms CPU = 0.004 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0989732 5.0989732 3.6203867 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.552248 0.0000000) to (28.276124 56.552248 3.6203867) create_atoms CPU = 0.003 seconds 490 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_390178379548_001#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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3276.4144 0 -3276.4144 48416.627 98 0 -3455.3549 0 -3455.3549 6048.1223 Loop time of 7.26856 on 1 procs for 98 steps with 978 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3276.41442185521 -3455.35167593346 -3455.35492478865 Force two-norm initial, final = 209.82918 0.17069590 Force max component initial, final = 35.508107 0.041022244 Final line search alpha, max atom move = 1.0000000 0.041022244 Iterations, force evaluations = 98 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1979 | 7.1979 | 7.1979 | 0.0 | 99.03 Neigh | 0.02354 | 0.02354 | 0.02354 | 0.0 | 0.32 Comm | 0.024464 | 0.024464 | 0.024464 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02265 | | | 0.31 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5194.00 ave 5194 max 5194 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: 75888.0 ave 75888 max 75888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75888 Ave neighs/atom = 77.595092 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -3455.3549 0 -3455.3549 6048.1223 11578.564 104 0 -3455.5559 0 -3455.5559 -203.94619 11628.564 Loop time of 0.361169 on 1 procs for 6 steps with 978 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 = -3455.35492478865 -3455.55513955909 -3455.55590466039 Force two-norm initial, final = 90.928588 3.8378566 Force max component initial, final = 82.320997 3.4340544 Final line search alpha, max atom move = 0.00023024224 0.00079066439 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35629 | 0.35629 | 0.35629 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010817 | 0.0010817 | 0.0010817 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003793 | | | 1.05 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 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: 75852.0 ave 75852 max 75852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75852 Ave neighs/atom = 77.558282 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.726 | 4.726 | 4.726 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3455.5559 0 -3455.5559 -203.94619 Loop time of 6.254e-06 on 1 procs for 0 steps with 978 atoms 191.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5194.00 ave 5194 max 5194 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: 75852.0 ave 75852 max 75852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75852 Ave neighs/atom = 77.558282 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.726 | 4.726 | 4.726 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 -3455.5559 -3455.5559 28.247269 113.67901 3.6213404 -203.94619 -203.94619 82.024824 -220.59682 -473.26656 2.3130474 160.99906 Loop time of 6.826e-06 on 1 procs for 0 steps with 978 atoms 249.0% 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 | | 6.826e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5194.00 ave 5194 max 5194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37926.0 ave 37926 max 37926 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75852.0 ave 75852 max 75852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75852 Ave neighs/atom = 77.558282 Neighbor list builds = 0 Dangerous builds = 0 978 -3455.55590466039 eV 2.31304743918873 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08