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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -43.242276 0.0000000) to (30.576907 43.242276 5.7275794) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9008065 6.8277278 5.7275794 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -43.242276 0.0000000) to (30.576907 43.242276 5.7275794) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9008065 6.8277278 5.7275794 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.242276 0.0000000) to (30.576907 43.242276 5.7275794) create_atoms CPU = 0.001 seconds 458 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 23 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 910 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_120808805541_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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.962 | 4.962 | 4.962 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2860.5599 0 -2860.5599 35058.683 74 0 -3073.9251 0 -3073.9251 3597.551 Loop time of 0.73026 on 1 procs for 74 steps with 910 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 = -2860.55986606196 -3073.92226042196 -3073.92505621386 Force two-norm initial, final = 344.41750 0.13754698 Force max component initial, final = 89.020391 0.031527988 Final line search alpha, max atom move = 1.0000000 0.031527988 Iterations, force evaluations = 74 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70392 | 0.70392 | 0.70392 | 0.0 | 96.39 Neigh | 0.013495 | 0.013495 | 0.013495 | 0.0 | 1.85 Comm | 0.0067562 | 0.0067562 | 0.0067562 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006085 | | | 0.83 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4754.00 ave 4754 max 4754 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: 110376.0 ave 110376 max 110376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110376 Ave neighs/atom = 121.29231 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.962 | 4.962 | 4.962 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -3073.9251 0 -3073.9251 3597.551 15146.183 79 0 -3074.0474 0 -3074.0474 -17.527969 15217.275 Loop time of 0.0376519 on 1 procs for 5 steps with 910 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 = -3073.92505621386 -3074.04731436411 -3074.04736038668 Force two-norm initial, final = 64.522633 0.34697965 Force max component initial, final = 54.068502 0.22686715 Final line search alpha, max atom move = 0.0013256114 0.00030073768 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035964 | 0.035964 | 0.035964 | 0.0 | 95.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027401 | 0.00027401 | 0.00027401 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001414 | | | 3.76 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676.00 ave 4676 max 4676 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: 112012.0 ave 112012 max 112012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112012 Ave neighs/atom = 123.09011 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.100 | 5.100 | 5.100 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3074.0474 0 -3074.0474 -17.527969 Loop time of 1.872e-06 on 1 procs for 0 steps with 910 atoms 106.8% 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 | | 1.872e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676.00 ave 4676 max 4676 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: 106948.0 ave 106948 max 106948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106948 Ave neighs/atom = 117.52527 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.100 | 5.100 | 5.100 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 -3074.0474 -3074.0474 30.611088 86.838772 5.724591 -17.527969 -17.527969 -23.912792 -14.81689 -13.854224 2.6344904 847.92515 Loop time of 1.876e-06 on 1 procs for 0 steps with 910 atoms 213.2% 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 | | 1.876e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4676.00 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53474.0 ave 53474 max 53474 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106948.0 ave 106948 max 106948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106948 Ave neighs/atom = 117.52527 Neighbor list builds = 0 Dangerous builds = 0 910 -3074.04736038668 eV 2.63449037925442 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01