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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -65.986909 0.0000000) to (13.469521 65.986909 9.9479008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1225097 5.9988099 6.6319338 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -65.986909 0.0000000) to (13.469521 65.986909 9.9479008) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1225097 5.9988099 6.6319338 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.986909 0.0000000) to (13.469521 65.986909 9.9479008) create_atoms CPU = 0.001 seconds 530 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 27 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1052 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.552 | 5.552 | 5.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2619.6984 0 -2619.6984 16795.015 81 0 -2826.924 0 -2826.924 198.85304 Loop time of 1.34285 on 1 procs for 81 steps with 1052 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 = -2619.69844510856 -2826.9214246608 -2826.9240241225 Force two-norm initial, final = 295.21286 0.16231975 Force max component initial, final = 96.498329 0.023759079 Final line search alpha, max atom move = 1.0000000 0.023759079 Iterations, force evaluations = 81 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.279 | 1.279 | 1.279 | 0.0 | 95.25 Neigh | 0.048707 | 0.048707 | 0.048707 | 0.0 | 3.63 Comm | 0.0080082 | 0.0080082 | 0.0080082 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007089 | | | 0.53 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7573.00 ave 7573 max 7573 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: 235372.0 ave 235372 max 235372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235372 Ave neighs/atom = 223.73764 Neighbor list builds = 3 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.552 | 5.552 | 5.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -2826.924 0 -2826.924 198.85304 17683.629 83 0 -2826.9351 0 -2826.9351 91.039325 17686.197 Loop time of 0.0393503 on 1 procs for 2 steps with 1052 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 = -2826.92402412248 -2826.93437789989 -2826.93505289243 Force two-norm initial, final = 15.905105 2.2564945 Force max component initial, final = 14.050475 2.0804725 Final line search alpha, max atom move = 0.00029274878 0.00060905580 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038261 | 0.038261 | 0.038261 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021717 | 0.00021717 | 0.00021717 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008722 | | | 2.22 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7615.00 ave 7615 max 7615 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: 235644.0 ave 235644 max 235644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235644 Ave neighs/atom = 223.99620 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.690 | 5.690 | 5.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2826.9351 0 -2826.9351 91.039325 Loop time of 1.519e-06 on 1 procs for 0 steps with 1052 atoms 131.7% 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 | | 1.519e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7597.00 ave 7597 max 7597 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: 235588.0 ave 235588 max 235588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235588 Ave neighs/atom = 223.94297 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.690 | 5.690 | 5.690 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 -2826.9351 -2826.9351 13.466559 132.11607 9.9408193 91.039325 91.039325 7.1976123 188.67125 77.249111 2.5693445 524.32852 Loop time of 1.76e-06 on 1 procs for 0 steps with 1052 atoms 227.3% 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 | | 1.76e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7597.00 ave 7597 max 7597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117794.0 ave 117794 max 117794 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235588.0 ave 235588 max 235588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235588 Ave neighs/atom = 223.94297 Neighbor list builds = 0 Dangerous builds = 0 1052 -2826.93505289243 eV 2.56934454717095 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01