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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -43.978527 0.0000000) to (21.989264 43.978527 3.6150127) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1601310 4.1601310 3.6150127 Created 295 atoms using lattice units in orthogonal box = (0.0000000 -43.978527 0.0000000) to (21.989264 43.978527 3.6150127) create_atoms CPU = 0.002 seconds 295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1601310 4.1601310 3.6150127 Created 297 atoms using lattice units in orthogonal box = (0.0000000 -43.978527 0.0000000) to (21.989264 43.978527 3.6150127) create_atoms CPU = 0.002 seconds 297 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 592 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_028979335952_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1935.8608 0 -1935.8608 59913.276 54 0 -2084.08 0 -2084.08 7277.6409 Loop time of 8.52494 on 1 procs for 54 steps with 592 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 = -1935.86078356449 -2084.07844077486 -2084.08000363598 Force two-norm initial, final = 172.50901 0.13145028 Force max component initial, final = 42.336777 0.027965539 Final line search alpha, max atom move = 1.0000000 0.027965539 Iterations, force evaluations = 54 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4954 | 8.4954 | 8.4954 | 0.0 | 99.65 Neigh | 0.0093511 | 0.0093511 | 0.0093511 | 0.0 | 0.11 Comm | 0.011242 | 0.011242 | 0.011242 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008969 | | | 0.11 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4962.00 ave 4962 max 4962 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: 78022.0 ave 78022 max 78022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78022 Ave neighs/atom = 131.79392 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2084.08 0 -2084.08 7277.6409 6991.8352 57 0 -2084.163 0 -2084.163 -0.22149783 7027.7381 Loop time of 0.539115 on 1 procs for 3 steps with 592 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 = -2084.08000363598 -2084.16192164309 -2084.16297496938 Force two-norm initial, final = 55.113560 0.14698261 Force max component initial, final = 34.470443 0.033551596 Final line search alpha, max atom move = 0.00049283151 1.6535284e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53673 | 0.53673 | 0.53673 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057246 | 0.00057246 | 0.00057246 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001816 | | | 0.34 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4453.00 ave 4453 max 4453 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: 78402.0 ave 78402 max 78402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78402 Ave neighs/atom = 132.43581 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2084.163 0 -2084.163 -0.22149783 Loop time of 6.304e-06 on 1 procs for 0 steps with 592 atoms 174.5% 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 | | 6.304e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4453.00 ave 4453 max 4453 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: 78276.0 ave 78276 max 78276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78276 Ave neighs/atom = 132.22297 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.647 | 4.647 | 4.647 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 -2084.163 -2084.163 22.02071 88.055311 3.6243381 -0.22149783 -0.22149783 3.6369609 -2.367252 -1.9342025 2.2962129 193.52711 Loop time of 6.576e-06 on 1 procs for 0 steps with 592 atoms 288.9% 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 | | 6.576e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4453.00 ave 4453 max 4453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39138.0 ave 39138 max 39138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78276.0 ave 78276 max 78276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78276 Ave neighs/atom = 132.22297 Neighbor list builds = 0 Dangerous builds = 0 592 -2084.16297496938 eV 2.29621288040517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09