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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -41.809270 0.0000000) to (29.563619 41.809270 5.1463654) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2710706 5.7012641 5.1463654 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.809270 0.0000000) to (29.563619 41.809270 5.1463654) create_atoms CPU = 0.004 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2710706 5.7012641 5.1463654 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.809270 0.0000000) to (29.563619 41.809270 5.1463654) create_atoms CPU = 0.003 seconds 532 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_748636486270_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2833.7563 0 -2833.7563 158188.58 74 0 -3602.9278 0 -3602.9278 4681.3665 Loop time of 3.00498 on 1 procs for 74 steps with 1056 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 = -2833.75633860696 -3602.92557263195 -3602.92783440789 Force two-norm initial, final = 1520.8941 0.11290825 Force max component initial, final = 329.19972 0.0066039700 Final line search alpha, max atom move = 1.0000000 0.0066039700 Iterations, force evaluations = 74 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9139 | 2.9139 | 2.9139 | 0.0 | 96.97 Neigh | 0.050626 | 0.050626 | 0.050626 | 0.0 | 1.68 Comm | 0.021818 | 0.021818 | 0.021818 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01866 | | | 0.62 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6786.00 ave 6786 max 6786 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: 185776.0 ave 185776 max 185776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185776 Ave neighs/atom = 175.92424 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -3602.9278 0 -3602.9278 4681.3665 12722.158 78 0 -3603.0375 0 -3603.0375 -205.42743 12764.976 Loop time of 0.131184 on 1 procs for 4 steps with 1056 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 = -3602.92783440788 -3603.0364220619 -3603.03745994793 Force two-norm initial, final = 73.038661 3.8948383 Force max component initial, final = 57.534751 3.5868416 Final line search alpha, max atom move = 0.00017789882 0.00063809489 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12738 | 0.12738 | 0.12738 | 0.0 | 97.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086587 | 0.00086587 | 0.00086587 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002943 | | | 2.24 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6784.00 ave 6784 max 6784 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: 185160.0 ave 185160 max 185160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185160 Ave neighs/atom = 175.34091 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.165 | 5.165 | 5.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3603.0375 0 -3603.0375 -205.42743 Loop time of 6.746e-06 on 1 procs for 0 steps with 1056 atoms 177.9% 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 | | 6.746e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6752.00 ave 6752 max 6752 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: 184992.0 ave 184992 max 184992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184992 Ave neighs/atom = 175.18182 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.165 | 5.165 | 5.165 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 -3603.0375 -3603.0375 29.63915 83.778147 5.1407149 -205.42743 -205.42743 -188.72873 22.149091 -449.70265 2.4051081 739.70604 Loop time of 6.966e-06 on 1 procs for 0 steps with 1056 atoms 272.8% 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 | | 6.966e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6752.00 ave 6752 max 6752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92496.0 ave 92496 max 92496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184992.0 ave 184992 max 184992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184992 Ave neighs/atom = 175.18182 Neighbor list builds = 0 Dangerous builds = 0 1056 -3603.03745994793 eV 2.40510811522754 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03