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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -43.828637 0.0000000) to (35.785933 43.828637 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1122761 5.0686179 5.9031479 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.828637 0.0000000) to (35.785933 43.828637 8.8547219) create_atoms CPU = 0.005 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1122761 5.0686179 5.9031479 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.828637 0.0000000) to (35.785933 43.828637 8.8547219) create_atoms CPU = 0.004 seconds 1184 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.023 | 6.023 | 6.023 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7788.0633 0 -7788.0633 48902.782 80 0 -8231.8921 0 -8231.8921 -1526.9919 Loop time of 5.25027 on 1 procs for 80 steps with 2336 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 = -7788.06330233405 -8231.88455308753 -8231.89207174821 Force two-norm initial, final = 655.98329 0.27226960 Force max component initial, final = 106.22644 0.042505927 Final line search alpha, max atom move = 1.0000000 0.042505927 Iterations, force evaluations = 80 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0759 | 5.0759 | 5.0759 | 0.0 | 96.68 Neigh | 0.10601 | 0.10601 | 0.10601 | 0.0 | 2.02 Comm | 0.030876 | 0.030876 | 0.030876 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03748 | | | 0.71 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8371.00 ave 8371 max 8371 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: 330688.0 ave 330688 max 330688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330688 Ave neighs/atom = 141.56164 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.021 | 6.021 | 6.021 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -8231.8921 0 -8231.8921 -1526.9919 27776.354 83 0 -8231.9705 0 -8231.9705 297.77082 27739.343 Loop time of 0.161431 on 1 procs for 3 steps with 2336 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8231.89207174819 -8231.96669258378 -8231.97052315735 Force two-norm initial, final = 67.907005 11.806864 Force max component initial, final = 60.305966 11.449291 Final line search alpha, max atom move = 7.7905839e-05 0.00089196661 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15693 | 0.15693 | 0.15693 | 0.0 | 97.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084434 | 0.00084434 | 0.00084434 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003657 | | | 2.27 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8081.00 ave 8081 max 8081 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: 330032.0 ave 330032 max 330032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330032 Ave neighs/atom = 141.28082 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.160 | 6.160 | 6.160 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8231.9705 0 -8231.9705 297.77082 Loop time of 6.445e-06 on 1 procs for 0 steps with 2336 atoms 186.2% 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 | | 6.445e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8267.00 ave 8267 max 8267 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: 330208.0 ave 330208 max 330208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330208 Ave neighs/atom = 141.35616 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.160 | 6.160 | 6.160 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 -8231.9705 -8231.9705 35.759397 87.76932 8.8381885 297.77082 297.77082 97.95434 662.13651 133.22161 2.2982852 1335.145 Loop time of 6.976e-06 on 1 procs for 0 steps with 2336 atoms 286.7% 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 | | 6.976e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8267.00 ave 8267 max 8267 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165104.0 ave 165104 max 165104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 330208.0 ave 330208 max 330208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330208 Ave neighs/atom = 141.35616 Neighbor list builds = 0 Dangerous builds = 0 2336 -8231.98220315735 eV 2.29828524620136 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06