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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -47.920367 0.0000000) to (58.690224 47.920367 9.9204585) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074542 6.1611901 6.6136390 Created 1659 atoms using lattice units in orthogonal box = (0.0000000 -47.920367 0.0000000) to (58.690224 47.920367 9.9204585) create_atoms CPU = 0.003 seconds 1659 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074542 6.1611901 6.6136390 Created 1683 atoms using lattice units in orthogonal box = (0.0000000 -47.920367 0.0000000) to (58.690224 47.920367 9.9204585) create_atoms CPU = 0.002 seconds 1683 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 16 26 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 27 atoms, new total = 3315 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_120808805541_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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.466 | 6.466 | 6.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11131.883 0 -11131.883 2918.2458 93 0 -11202.361 0 -11202.361 -6814.8922 Loop time of 2.89447 on 1 procs for 93 steps with 3315 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11131.8825892205 -11202.3514246652 -11202.3606446584 Force two-norm initial, final = 50.835717 0.24575608 Force max component initial, final = 8.0965267 0.045910354 Final line search alpha, max atom move = 1.0000000 0.045910354 Iterations, force evaluations = 93 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7072 | 2.7072 | 2.7072 | 0.0 | 93.53 Neigh | 0.13962 | 0.13962 | 0.13962 | 0.0 | 4.82 Comm | 0.018043 | 0.018043 | 0.018043 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02959 | | | 1.02 Nlocal: 3315.00 ave 3315 max 3315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9146.00 ave 9146 max 9146 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: 347068.0 ave 347068 max 347068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 347068 Ave neighs/atom = 104.69623 Neighbor list builds = 5 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -11202.361 0 -11202.361 -6814.8922 55801.727 100 0 -11203.575 0 -11203.575 -4.7893019 55298.371 Loop time of 0.181264 on 1 procs for 7 steps with 3315 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 = -11202.3606446584 -11203.5712902547 -11203.5750148558 Force two-norm initial, final = 417.77595 0.80149555 Force max component initial, final = 297.77078 0.68607092 Final line search alpha, max atom move = 4.1232110e-05 2.8288152e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.174 | 0.174 | 0.174 | 0.0 | 96.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088352 | 0.00088352 | 0.00088352 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006376 | | | 3.52 Nlocal: 3315.00 ave 3315 max 3315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9142.00 ave 9142 max 9142 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: 346076.0 ave 346076 max 346076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346076 Ave neighs/atom = 104.39698 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.606 | 6.606 | 6.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11203.575 0 -11203.575 -4.7893019 Loop time of 2.185e-06 on 1 procs for 0 steps with 3315 atoms 183.1% 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 | | 2.185e-06 | | |100.00 Nlocal: 3315.00 ave 3315 max 3315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9153.00 ave 9153 max 9153 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: 394990.0 ave 394990 max 394990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394990 Ave neighs/atom = 119.15234 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.606 | 6.606 | 6.606 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 -11203.575 -11203.575 58.579424 95.274219 9.9081333 -4.7893019 -4.7893019 -19.840214 0.7437564 4.7285525 2.5757546 2219.017 Loop time of 3.063e-06 on 1 procs for 0 steps with 3315 atoms 261.2% 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 | | 3.063e-06 | | |100.00 Nlocal: 3315.00 ave 3315 max 3315 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9153.00 ave 9153 max 9153 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 197495.0 ave 197495 max 197495 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 394990.0 ave 394990 max 394990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394990 Ave neighs/atom = 119.15234 Neighbor list builds = 0 Dangerous builds = 0 3315 -11203.5750148558 eV 2.57575457337626 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03