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 = 4.0499992 4.0499992 4.0499992 Created orthogonal box = (0.0000000 -52.498039 0.0000000) to (30.307419 52.498039 7.0148043) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4944469 6.2492844 7.0148043 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.498039 0.0000000) to (30.307419 52.498039 7.0148043) create_atoms CPU = 0.006 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4944469 6.2492844 7.0148043 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.498039 0.0000000) to (30.307419 52.498039 7.0148043) create_atoms CPU = 0.005 seconds 676 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 = 9 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 1320 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_262519520678_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 = 9 30 3 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4389.183 0 -4389.183 -995.05563 42 0 -4408.5178 0 -4408.5178 -9627.9632 Loop time of 9.80146 on 1 procs for 42 steps with 1320 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 = -4389.18297980902 -4408.51388912251 -4408.51783637164 Force two-norm initial, final = 10.462891 0.17147242 Force max component initial, final = 1.3884287 0.012008384 Final line search alpha, max atom move = 1.0000000 0.012008384 Iterations, force evaluations = 42 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7459 | 9.7459 | 9.7459 | 0.0 | 99.43 Neigh | 0.034543 | 0.034543 | 0.034543 | 0.0 | 0.35 Comm | 0.009132 | 0.009132 | 0.009132 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01189 | | | 0.12 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5256.00 ave 5256 max 5256 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: 103008.0 ave 103008 max 103008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103008 Ave neighs/atom = 78.036364 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 30 3 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -4408.5178 0 -4408.5178 -9627.9632 22322.23 48 0 -4409.0898 0 -4409.0898 -2242.5538 22102.109 Loop time of 1.2715 on 1 procs for 6 steps with 1320 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 = -4408.51783637163 -4409.08745746878 -4409.08984709709 Force two-norm initial, final = 162.79657 2.8616140 Force max component initial, final = 120.23690 2.6650463 Final line search alpha, max atom move = 0.00010631222 0.00028332698 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2657 | 1.2657 | 1.2657 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099441 | 0.00099441 | 0.00099441 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004775 | | | 0.38 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5256.00 ave 5256 max 5256 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: 102976.0 ave 102976 max 102976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102976 Ave neighs/atom = 78.012121 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 = 9 30 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) = 5.200 | 5.200 | 5.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4409.0898 0 -4409.0898 -2242.5538 Loop time of 6.205e-06 on 1 procs for 0 steps with 1320 atoms 193.4% 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 | | 6.205e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5256.00 ave 5256 max 5256 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: 107960.0 ave 107960 max 107960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107960 Ave neighs/atom = 81.787879 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 = 9 30 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) = 5.200 | 5.200 | 5.200 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 -4409.0898 -4409.0898 30.142421 104.99608 6.9836508 -2242.5538 -2242.5538 -73.162575 -6846.8295 192.33058 2.6117154 1018.4678 Loop time of 7.137e-06 on 1 procs for 0 steps with 1320 atoms 280.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5256.00 ave 5256 max 5256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53980.0 ave 53980 max 53980 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107960.0 ave 107960 max 107960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107960 Ave neighs/atom = 81.787879 Neighbor list builds = 0 Dangerous builds = 0 1320 -4409.08984709713 eV 2.61171543013956 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12