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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -36.694868 0.0000000) to (12.973595 36.694868 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3420685 5.3963041 4.4499064 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -36.694868 0.0000000) to (12.973595 36.694868 4.4499064) create_atoms CPU = 0.001 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3420685 5.3963041 4.4499064 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -36.694868 0.0000000) to (12.973595 36.694868 4.4499064) create_atoms CPU = 0.000 seconds 138 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 272 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.417 | 4.417 | 4.417 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1682.5471 0 -1682.5471 160125.67 46 0 -1839.2531 0 -1839.2531 13301.228 Loop time of 0.807831 on 1 procs for 46 steps with 272 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 = -1682.54706241552 -1839.25198980564 -1839.2530544033 Force two-norm initial, final = 223.03764 0.19240424 Force max component initial, final = 74.683243 0.042899722 Final line search alpha, max atom move = 1.0000000 0.042899722 Iterations, force evaluations = 46 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80451 | 0.80451 | 0.80451 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018446 | 0.0018446 | 0.0018446 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001481 | | | 0.18 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2376.00 ave 2376 max 2376 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: 17884.0 ave 17884 max 17884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17884 Ave neighs/atom = 65.750000 Neighbor list builds = 0 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.419 | 4.419 | 4.419 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1839.2531 0 -1839.2531 13301.228 4236.8836 53 0 -1839.4505 0 -1839.4505 -371.28618 4258.7352 Loop time of 0.0846222 on 1 procs for 7 steps with 272 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 = -1839.2530544033 -1839.4498519512 -1839.45053824521 Force two-norm initial, final = 71.337544 1.8227199 Force max component initial, final = 64.563032 1.1841153 Final line search alpha, max atom move = 0.00034023518 0.00040287768 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08342 | 0.08342 | 0.08342 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021146 | 0.00021146 | 0.00021146 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009906 | | | 1.17 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2706.00 ave 2706 max 2706 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: 18096.0 ave 18096 max 18096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18096 Ave neighs/atom = 66.529412 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.557 | 4.557 | 4.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1839.4505 0 -1839.4505 -371.28618 Loop time of 1.82e-06 on 1 procs for 0 steps with 272 atoms 109.9% 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 | | 1.82e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2706.00 ave 2706 max 2706 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: 17976.0 ave 17976 max 17976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17976 Ave neighs/atom = 66.088235 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.557 | 4.557 | 4.557 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 -1839.4505 -1839.4505 12.977632 73.860145 4.4429867 -371.28618 -371.28618 -445.61402 -228.84665 -439.39787 2.4429023 225.19407 Loop time of 1.819e-06 on 1 procs for 0 steps with 272 atoms 110.0% 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 | | 1.819e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2706.00 ave 2706 max 2706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8988.00 ave 8988 max 8988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17976.0 ave 17976 max 17976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17976 Ave neighs/atom = 66.088235 Neighbor list builds = 0 Dangerous builds = 0 272 -1839.45053824521 eV 2.44290229694168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01