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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -36.203620 0.0000000) to (18.100000 36.203620 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0680000 5.0680000 3.6200000 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.203620 0.0000000) to (18.100000 36.203620 3.6200000) create_atoms CPU = 0.001 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0680000 5.0680000 3.6200000 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.203620 0.0000000) to (18.100000 36.203620 3.6200000) create_atoms CPU = 0.001 seconds 201 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 = 6 21 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 4 atoms, new total = 398 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 = 6 21 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1379.2374 0 -1379.2374 21917.296 56 0 -1403.4805 0 -1403.4805 -683.93656 Loop time of 5.50795 on 1 procs for 56 steps with 398 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 = -1379.23741545128 -1403.47926602189 -1403.48054909145 Force two-norm initial, final = 32.334872 0.095378857 Force max component initial, final = 11.608542 0.017975633 Final line search alpha, max atom move = 1.0000000 0.017975633 Iterations, force evaluations = 56 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4864 | 5.4864 | 5.4864 | 0.0 | 99.61 Neigh | 0.0065773 | 0.0065773 | 0.0065773 | 0.0 | 0.12 Comm | 0.0080906 | 0.0080906 | 0.0080906 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006897 | | | 0.13 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3822.00 ave 3822 max 3822 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: 52480.0 ave 52480 max 52480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52480 Ave neighs/atom = 131.85930 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 = 6 21 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -1403.4805 0 -1403.4805 -683.93656 4744.2673 58 0 -1403.4859 0 -1403.4859 1410.6947 4737.0232 Loop time of 0.309954 on 1 procs for 2 steps with 398 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 = -1403.48054909145 -1403.48573156417 -1403.48588579068 Force two-norm initial, final = 9.8109568 0.10065159 Force max component initial, final = 7.0309114 0.020534625 Final line search alpha, max atom move = 0.0016597149 3.4081623e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30833 | 0.30833 | 0.30833 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039331 | 0.00039331 | 0.00039331 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001233 | | | 0.40 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3812.00 ave 3812 max 3812 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: 52624.0 ave 52624 max 52624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52624 Ave neighs/atom = 132.22111 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 = 6 21 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1403.4859 0 -1403.4859 1410.6947 Loop time of 6.565e-06 on 1 procs for 0 steps with 398 atoms 182.8% 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 | | 6.565e-06 | | |100.00 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3817.00 ave 3817 max 3817 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: 52632.0 ave 52632 max 52632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52632 Ave neighs/atom = 132.24121 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 = 6 21 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) = 4.594 | 4.594 | 4.594 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 -1403.4859 -1403.4859 18.091257 72.40724 3.6162193 1410.6947 1410.6947 -6.0567022 4236.616 1.5248647 2.2886065 161.64895 Loop time of 6.997e-06 on 1 procs for 0 steps with 398 atoms 243.0% 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 | | 6.997e-06 | | |100.00 Nlocal: 398.000 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3817.00 ave 3817 max 3817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26316.0 ave 26316 max 26316 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52632.0 ave 52632 max 52632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52632 Ave neighs/atom = 132.24121 Neighbor list builds = 0 Dangerous builds = 0 398 -1403.48588579068 eV 2.28860647799482 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06