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 = 4.0501807 4.0501807 4.0501807 Created orthogonal box = (0.0000000 -43.244097 0.0000000) to (30.578194 43.244097 5.7278205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9010550 6.8280153 5.7278205 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -43.244097 0.0000000) to (30.578194 43.244097 5.7278205) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9010550 6.8280153 5.7278205 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.244097 0.0000000) to (30.578194 43.244097 5.7278205) 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, 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 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_131650261510_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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3182.2198 0 -3182.2198 9602.4033 65 0 -3244.224 0 -3244.224 4597.5725 Loop time of 0.967852 on 1 procs for 65 steps with 908 atoms 90.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3182.21976211618 -3244.2210747167 -3244.22397913702 Force two-norm initial, final = 83.489972 0.11199416 Force max component initial, final = 24.742770 0.0081918260 Final line search alpha, max atom move = 1.0000000 0.0081918260 Iterations, force evaluations = 65 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91804 | 0.91804 | 0.91804 | 0.0 | 94.85 Neigh | 0.038089 | 0.038089 | 0.038089 | 0.0 | 3.94 Comm | 0.0062575 | 0.0062575 | 0.0062575 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005467 | | | 0.56 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5756.00 ave 5756 max 5756 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: 127248.0 ave 127248 max 127248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127248 Ave neighs/atom = 140.14097 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -3244.224 0 -3244.224 4597.5725 15148.096 72 0 -3244.412 0 -3244.412 34.015476 15239.244 Loop time of 0.0614001 on 1 procs for 7 steps with 908 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 = -3244.22397913702 -3244.41136365766 -3244.41202081502 Force two-norm initial, final = 79.739058 1.0101474 Force max component initial, final = 64.909262 0.94723009 Final line search alpha, max atom move = 0.00043087438 0.00040813718 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059256 | 0.059256 | 0.059256 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040134 | 0.00040134 | 0.00040134 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001743 | | | 2.84 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754.00 ave 5754 max 5754 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: 127308.0 ave 127308 max 127308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127308 Ave neighs/atom = 140.20705 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 5.120 | 5.120 | 5.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3244.412 0 -3244.412 34.015476 Loop time of 1.566e-06 on 1 procs for 0 steps with 908 atoms 127.7% 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 | | 1.566e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754.00 ave 5754 max 5754 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: 127092.0 ave 127092 max 127092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127092 Ave neighs/atom = 139.96916 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 5.120 | 5.120 | 5.120 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 -3244.412 -3244.412 30.5766 87.006516 5.7282564 34.015476 34.015476 -21.661176 100.18377 23.523833 2.6530615 773.00174 Loop time of 1.831e-06 on 1 procs for 0 steps with 908 atoms 163.8% 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 | | 1.831e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754.00 ave 5754 max 5754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63546.0 ave 63546 max 63546 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127092.0 ave 127092 max 127092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127092 Ave neighs/atom = 139.96916 Neighbor list builds = 0 Dangerous builds = 0 908 -3244.41115487874 eV 2.6530614645303 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01