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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -56.434784 0.0000000) to (34.557361 56.434784 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9964295 4.0308524 4.6544275 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.434784 0.0000000) to (34.557361 56.434784 6.9816412) create_atoms CPU = 0.002 seconds 1182 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9964295 4.0308524 4.6544275 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.434784 0.0000000) to (34.557361 56.434784 6.9816412) create_atoms CPU = 0.001 seconds 1182 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 2328 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9909.2432 0 -9909.2432 -2506.4179 66 0 -9950.0569 0 -9950.0569 -10849.946 Loop time of 16.3161 on 1 procs for 66 steps with 2328 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 = -9909.24324728042 -9950.04923097992 -9950.05689431966 Force two-norm initial, final = 38.565241 0.25926251 Force max component initial, final = 7.9683794 0.038803383 Final line search alpha, max atom move = 1.0000000 0.038803383 Iterations, force evaluations = 66 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.28 | 16.28 | 16.28 | 0.0 | 99.78 Neigh | 0.013663 | 0.013663 | 0.013663 | 0.0 | 0.08 Comm | 0.0086168 | 0.0086168 | 0.0086168 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0136 | | | 0.08 Nlocal: 2328.00 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7513.00 ave 7513 max 7513 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: 150588.0 ave 150588 max 150588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150588 Ave neighs/atom = 64.685567 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.231 | 5.231 | 5.231 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -9950.0569 0 -9950.0569 -10849.946 27231.713 70 0 -9950.6401 0 -9950.6401 -898.18961 27066.101 Loop time of 0.798369 on 1 procs for 4 steps with 2328 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 = -9950.0568943198 -9950.63760551593 -9950.6401146989 Force two-norm initial, final = 271.49026 5.1025956 Force max component initial, final = 195.23196 4.9463215 Final line search alpha, max atom move = 6.3078272e-05 0.00031200542 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79609 | 0.79609 | 0.79609 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031897 | 0.00031897 | 0.00031897 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001959 | | | 0.25 Nlocal: 2328.00 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6946.00 ave 6946 max 6946 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: 150444.0 ave 150444 max 150444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150444 Ave neighs/atom = 64.623711 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.369 | 5.369 | 5.369 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9950.6401 0 -9950.6401 -898.18961 Loop time of 1.869e-06 on 1 procs for 0 steps with 2328 atoms 214.0% 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 | | 1.869e-06 | | |100.00 Nlocal: 2328.00 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6948.00 ave 6948 max 6948 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: 150552.0 ave 150552 max 150552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150552 Ave neighs/atom = 64.670103 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.369 | 5.369 | 5.369 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 -9950.6401 -9950.6401 34.443372 112.86957 6.9621469 -898.18961 -898.18961 -71.745245 -2914.8033 291.9797 2.2185309 936.91902 Loop time of 1.884e-06 on 1 procs for 0 steps with 2328 atoms 212.3% 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 | | 1.884e-06 | | |100.00 Nlocal: 2328.00 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6948.00 ave 6948 max 6948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75276.0 ave 75276 max 75276 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 150552.0 ave 150552 max 150552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150552 Ave neighs/atom = 64.670103 Neighbor list builds = 0 Dangerous builds = 0 2328 -9950.6401146989 eV 2.21853087458793 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17