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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -63.823880 0.0000000) to (36.848734 63.823880 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6690360 5.7277841 6.2584463 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -63.823880 0.0000000) to (36.848734 63.823880 6.2584463) create_atoms CPU = 0.003 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6690360 5.7277841 6.2584463 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.823880 0.0000000) to (36.848734 63.823880 6.2584463) create_atoms CPU = 0.002 seconds 1251 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 40 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2498 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.716 | 5.716 | 5.716 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8379.8184 0 -8379.8184 43521.448 66 0 -8811.8656 0 -8811.8656 7174.7131 Loop time of 8.41182 on 1 procs for 66 steps with 2498 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 = -8379.81837521987 -8811.85843684743 -8811.86561045036 Force two-norm initial, final = 430.72990 0.30370062 Force max component initial, final = 134.71840 0.054065223 Final line search alpha, max atom move = 1.0000000 0.054065223 Iterations, force evaluations = 66 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3609 | 8.3609 | 8.3609 | 0.0 | 99.39 Neigh | 0.018305 | 0.018305 | 0.018305 | 0.0 | 0.22 Comm | 0.016517 | 0.016517 | 0.016517 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01612 | | | 0.19 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9860.00 ave 9860 max 9860 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: 215954.0 ave 215954 max 215954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215954 Ave neighs/atom = 86.450761 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.716 | 5.716 | 5.716 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -8811.8656 0 -8811.8656 7174.7131 29437.593 72 0 -8812.4822 0 -8812.4822 -48.583942 29586.644 Loop time of 0.568878 on 1 procs for 6 steps with 2498 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 = -8811.86561045039 -8812.48144843563 -8812.48223851539 Force two-norm initial, final = 262.43324 3.3093122 Force max component initial, final = 224.94084 3.1798828 Final line search alpha, max atom move = 0.00011130543 0.00035393821 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56425 | 0.56425 | 0.56425 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071757 | 0.00071757 | 0.00071757 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003915 | | | 0.69 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9887.00 ave 9887 max 9887 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: 215362.0 ave 215362 max 215362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215362 Ave neighs/atom = 86.213771 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.854 | 5.854 | 5.854 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8812.4822 0 -8812.4822 -48.583942 Loop time of 2.327e-06 on 1 procs for 0 steps with 2498 atoms 171.9% 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 | | 2.327e-06 | | |100.00 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9866.00 ave 9866 max 9866 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: 215178.0 ave 215178 max 215178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215178 Ave neighs/atom = 86.140112 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.854 | 5.854 | 5.854 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 -8812.4822 -8812.4822 36.894019 128.29859 6.2505447 -48.583942 -48.583942 -172.40869 -14.391718 41.048583 2.2810553 957.35546 Loop time of 2.668e-06 on 1 procs for 0 steps with 2498 atoms 262.4% 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 | | 2.668e-06 | | |100.00 Nlocal: 2498.00 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9866.00 ave 9866 max 9866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107589.0 ave 107589 max 107589 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215178.0 ave 215178 max 215178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215178 Ave neighs/atom = 86.140112 Neighbor list builds = 0 Dangerous builds = 0 2498 -8812.48223851539 eV 2.28105525985026 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09