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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -38.597639 0.0000000) to (22.284357 38.597639 6.2613638) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8643045 5.4172125 6.2613638 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.597639 0.0000000) to (22.284357 38.597639 6.2613638) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8643045 5.4172125 6.2613638 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.597639 0.0000000) to (22.284357 38.597639 6.2613638) create_atoms CPU = 0.001 seconds 458 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_346334655118_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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2900.265 0 -2900.265 93204.402 107 0 -3213.7385 0 -3213.7385 6819.6166 Loop time of 1.26691 on 1 procs for 107 steps with 912 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 = -2900.26503544447 -3213.73565670143 -3213.73850690582 Force two-norm initial, final = 952.61952 0.17000490 Force max component initial, final = 311.13860 0.021579961 Final line search alpha, max atom move = 1.0000000 0.021579961 Iterations, force evaluations = 107 195 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2219 | 1.2219 | 1.2219 | 0.0 | 96.45 Neigh | 0.026316 | 0.026316 | 0.026316 | 0.0 | 2.08 Comm | 0.0095161 | 0.0095161 | 0.0095161 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009191 | | | 0.73 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5188.00 ave 5188 max 5188 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: 128860.0 ave 128860 max 128860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128860 Ave neighs/atom = 141.29386 Neighbor list builds = 3 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -3213.7385 0 -3213.7385 6819.6166 10771.093 111 0 -3213.8687 0 -3213.8687 -0.68882325 10823.834 Loop time of 0.0443426 on 1 procs for 4 steps with 912 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 = -3213.73850690581 -3213.86832639781 -3213.86868965515 Force two-norm initial, final = 81.695997 0.22987209 Force max component initial, final = 55.297070 0.11072005 Final line search alpha, max atom move = 0.00023144024 2.5625076e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042708 | 0.042708 | 0.042708 | 0.0 | 96.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029375 | 0.00029375 | 0.00029375 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001341 | | | 3.02 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5184.00 ave 5184 max 5184 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: 128932.0 ave 128932 max 128932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128932 Ave neighs/atom = 141.37281 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3213.8687 0 -3213.8687 -0.68882325 Loop time of 2.336e-06 on 1 procs for 0 steps with 912 atoms 128.4% 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 | | 2.336e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5165.00 ave 5165 max 5165 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: 128776.0 ave 128776 max 128776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128776 Ave neighs/atom = 141.20175 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.132 | 5.132 | 5.132 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 -3213.8687 -3213.8687 22.341839 77.36821 6.2618068 -0.68882325 -0.68882325 10.509243 -16.425831 3.8501175 2.3480757 643.3198 Loop time of 2.186e-06 on 1 procs for 0 steps with 912 atoms 228.7% 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 | | 2.186e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5165.00 ave 5165 max 5165 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64388.0 ave 64388 max 64388 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128776.0 ave 128776 max 128776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128776 Ave neighs/atom = 141.20175 Neighbor list builds = 0 Dangerous builds = 0 912 -3213.86850642639 eV 2.34807572131656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01