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 = 4.0501996 4.0501996 4.0501996 Created orthogonal box = (0.0000000 -61.156673 0.0000000) to (43.244298 61.156673 5.7278472) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8280471 6.9740066 5.7278472 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -61.156673 0.0000000) to (43.244298 61.156673 5.7278472) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8280471 6.9740066 5.7278472 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -61.156673 0.0000000) to (43.244298 61.156673 5.7278472) create_atoms CPU = 0.002 seconds 916 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 30 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 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_060567868558_000#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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.577 | 5.577 | 5.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6425.2563 0 -6425.2563 9139.7695 42 0 -6523.282 0 -6523.282 4116.5901 Loop time of 1.07143 on 1 procs for 42 steps with 1824 atoms 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6425.2562782898 -6523.27618006587 -6523.28203110844 Force two-norm initial, final = 94.805180 0.17084717 Force max component initial, final = 18.798640 0.023421625 Final line search alpha, max atom move = 1.0000000 0.023421625 Iterations, force evaluations = 42 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0246 | 1.0246 | 1.0246 | 0.0 | 95.63 Neigh | 0.032821 | 0.032821 | 0.032821 | 0.0 | 3.06 Comm | 0.0070125 | 0.0070125 | 0.0070125 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006996 | | | 0.65 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8936.00 ave 8936 max 8936 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: 255528.0 ave 255528 max 255528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255528 Ave neighs/atom = 140.09211 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.578 | 5.578 | 5.578 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -6523.282 0 -6523.282 4116.5901 30296.617 50 0 -6523.7585 0 -6523.7585 13.185562 30461.06 Loop time of 0.138487 on 1 procs for 8 steps with 1824 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 = -6523.28203110847 -6523.75468189569 -6523.75847392518 Force two-norm initial, final = 156.24788 0.50009614 Force max component initial, final = 142.25608 0.26645487 Final line search alpha, max atom move = 0.00012974647 3.4571579e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13448 | 0.13448 | 0.13448 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067372 | 0.00067372 | 0.00067372 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003328 | | | 2.40 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8950.00 ave 8950 max 8950 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: 255568.0 ave 255568 max 255568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255568 Ave neighs/atom = 140.11404 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.716 | 5.716 | 5.716 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6523.7585 0 -6523.7585 13.185562 Loop time of 1.744e-06 on 1 procs for 0 steps with 1824 atoms 172.0% 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 | | 1.744e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8950.00 ave 8950 max 8950 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: 255312.0 ave 255312 max 255312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255312 Ave neighs/atom = 139.97368 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.716 | 5.716 | 5.716 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 -6523.7585 -6523.7585 43.20689 123.26401 5.7194692 13.185562 13.185562 14.002744 11.909169 13.644774 2.652227 945.50679 Loop time of 1.807e-06 on 1 procs for 0 steps with 1824 atoms 221.4% 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 | | 1.807e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8950.00 ave 8950 max 8950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127656.0 ave 127656 max 127656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255312.0 ave 255312 max 255312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255312 Ave neighs/atom = 139.97368 Neighbor list builds = 0 Dangerous builds = 0 1824 -6523.75847392518 eV 2.65222701595966 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01