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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -38.074622 0.0000000) to (12.691541 38.074622 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8813617 4.8813617 3.5200000 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -38.074622 0.0000000) to (12.691541 38.074622 3.5200000) create_atoms CPU = 0.001 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8813617 4.8813617 3.5200000 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.074622 0.0000000) to (12.691541 38.074622 3.5200000) create_atoms CPU = 0.000 seconds 158 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_444394830472_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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1305.3672 0 -1305.3672 77599.24 17 0 -1381.8733 0 -1381.8733 8956.8714 Loop time of 0.213105 on 1 procs for 17 steps with 312 atoms 94.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1305.36720135528 -1381.87291588627 -1381.87329913758 Force two-norm initial, final = 317.18623 1.1104441 Force max component initial, final = 118.54315 0.42847748 Final line search alpha, max atom move = 0.41963938 0.17980602 Iterations, force evaluations = 17 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21163 | 0.21163 | 0.21163 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077666 | 0.00077666 | 0.00077666 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006939 | | | 0.33 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2528.00 ave 2528 max 2528 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: 24440.0 ave 24440 max 24440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24440 Ave neighs/atom = 78.333333 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1381.8733 0 -1381.8733 8956.8714 3401.9082 24 0 -1381.982 0 -1381.982 -470.8302 3419.9656 Loop time of 0.0637482 on 1 procs for 7 steps with 312 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 = -1381.87329913758 -1381.98148014164 -1381.98198715291 Force two-norm initial, final = 41.370037 2.1399501 Force max component initial, final = 38.802366 1.4748163 Final line search alpha, max atom move = 0.00082783209 0.0012209002 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062559 | 0.062559 | 0.062559 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021223 | 0.00021223 | 0.00021223 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009768 | | | 1.53 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2528.00 ave 2528 max 2528 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: 24412.0 ave 24412 max 24412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24412 Ave neighs/atom = 78.243590 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1381.982 0 -1381.982 -470.8302 Loop time of 1.977e-06 on 1 procs for 0 steps with 312 atoms 151.7% 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 | | 1.977e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2528.00 ave 2528 max 2528 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: 24396.0 ave 24396 max 24396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24396 Ave neighs/atom = 78.192308 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.564 | 4.564 | 4.564 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 -1381.982 -1381.982 12.68544 76.598723 3.5196111 -470.8302 -470.8302 -279.88405 -694.99628 -437.61028 2.2239823 150.33344 Loop time of 1.767e-06 on 1 procs for 0 steps with 312 atoms 169.8% 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 | | 1.767e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2528.00 ave 2528 max 2528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12198.0 ave 12198 max 12198 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24396.0 ave 24396 max 24396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24396 Ave neighs/atom = 78.192308 Neighbor list builds = 0 Dangerous builds = 0 312 -1381.98198715291 eV 2.22398226722135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00