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 -54.987677 0.0000000) to (27.492079 54.987677 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9575880 4.9575880 3.5200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.987677 0.0000000) to (27.492079 54.987677 3.5200000) create_atoms CPU = 0.001 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9575880 4.9575880 3.5200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.987677 0.0000000) to (27.492079 54.987677 3.5200000) create_atoms CPU = 0.001 seconds 490 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.434 | 5.434 | 5.434 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4291.2034 0 -4291.2034 8403.0336 95 0 -4324.6123 0 -4324.6123 105.7394 Loop time of 2.58155 on 1 procs for 95 steps with 974 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4291.20341955623 -4324.60885793161 -4324.61230494644 Force two-norm initial, final = 20.285177 0.19900873 Force max component initial, final = 5.0447437 0.017865212 Final line search alpha, max atom move = 1.0000000 0.017865212 Iterations, force evaluations = 95 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5303 | 2.5303 | 2.5303 | 0.0 | 98.02 Neigh | 0.025972 | 0.025972 | 0.025972 | 0.0 | 1.01 Comm | 0.015612 | 0.015612 | 0.015612 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009658 | | | 0.37 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9200.00 ave 9200 max 9200 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: 240772.0 ave 240772 max 240772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240772 Ave neighs/atom = 247.19918 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.435 | 5.435 | 5.435 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -4324.6123 0 -4324.6123 105.7394 10642.548 98 0 -4324.6378 0 -4324.6378 254.94675 10641.634 Loop time of 0.0806228 on 1 procs for 3 steps with 974 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 = -4324.61230494644 -4324.63647776639 -4324.6378452894 Force two-norm initial, final = 21.955575 1.3128348 Force max component initial, final = 19.500018 1.2616146 Final line search alpha, max atom move = 0.00012371794 0.00015608436 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.078697 | 0.078697 | 0.078697 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036539 | 0.00036539 | 0.00036539 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001561 | | | 1.94 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9178.00 ave 9178 max 9178 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: 240808.0 ave 240808 max 240808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240808 Ave neighs/atom = 247.23614 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4324.6378 0 -4324.6378 254.94675 Loop time of 1.854e-06 on 1 procs for 0 steps with 974 atoms 161.8% 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 | | 1.854e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9178.00 ave 9178 max 9178 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: 240872.0 ave 240872 max 240872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240872 Ave neighs/atom = 247.30185 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.573 | 5.573 | 5.573 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 -4324.6378 -4324.6378 27.445396 109.97535 3.5256846 254.94675 254.94675 45.046883 529.54122 190.25213 2.2308295 147.44531 Loop time of 4.001e-06 on 1 procs for 0 steps with 974 atoms 200.0% 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 | | 4.001e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9178.00 ave 9178 max 9178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120436.0 ave 120436 max 120436 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240872.0 ave 240872 max 240872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240872 Ave neighs/atom = 247.30185 Neighbor list builds = 0 Dangerous builds = 0 974 -4324.6378452894 eV 2.23082950161633 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03