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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -67.494974 0.0000000) to (23.863077 67.494974 5.1464435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1045080 6.2786022 5.1464435 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -67.494974 0.0000000) to (23.863077 67.494974 5.1464435) create_atoms CPU = 0.007 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1045080 6.2786022 5.1464435 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -67.494974 0.0000000) to (23.863077 67.494974 5.1464435) create_atoms CPU = 0.006 seconds 690 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1372 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_600021860456_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.360 | 6.360 | 6.360 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4203.566 0 -4203.566 51359.794 56 0 -4496.057 0 -4496.057 -616.84817 Loop time of 4.35826 on 1 procs for 56 steps with 1372 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 = -4203.56599888909 -4496.05321223676 -4496.05704016949 Force two-norm initial, final = 768.46683 0.15349473 Force max component initial, final = 265.13456 0.010796648 Final line search alpha, max atom move = 1.0000000 0.010796648 Iterations, force evaluations = 56 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1545 | 4.1545 | 4.1545 | 0.0 | 95.32 Neigh | 0.16331 | 0.16331 | 0.16331 | 0.0 | 3.75 Comm | 0.023866 | 0.023866 | 0.023866 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0166 | | | 0.38 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 436800.0 ave 436800 max 436800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436800 Ave neighs/atom = 318.36735 Neighbor list builds = 3 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.365 | 6.365 | 6.365 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -4496.057 0 -4496.057 -616.84817 16578.112 57 0 -4496.0606 0 -4496.0606 273.32927 16567.852 Loop time of 0.178876 on 1 procs for 1 steps with 1372 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4496.05704016951 -4496.05704016951 -4496.06062209466 Force two-norm initial, final = 14.897233 7.2831200 Force max component initial, final = 13.348934 6.5990003 Final line search alpha, max atom move = 7.4912347e-05 0.00049434660 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17595 | 0.17595 | 0.17595 | 0.0 | 98.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096735 | 0.00096735 | 0.00096735 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001958 | | | 1.09 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 436700.0 ave 436700 max 436700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436700 Ave neighs/atom = 318.29446 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.503 | 6.503 | 6.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4496.0606 0 -4496.0606 273.32927 Loop time of 4.346e-05 on 1 procs for 0 steps with 1372 atoms 27.6% 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 | | 4.346e-05 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 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: 436740.0 ave 436740 max 436740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436740 Ave neighs/atom = 318.32362 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.503 | 6.503 | 6.503 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 -4496.0606 -4496.0606 23.863669 134.96129 5.1442227 273.32927 273.32927 638.16514 280.67632 -98.85366 2.3541349 370.49018 Loop time of 8.6e-06 on 1 procs for 0 steps with 1372 atoms 232.6% 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 | | 8.6e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12085.0 ave 12085 max 12085 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218370.0 ave 218370 max 218370 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436740.0 ave 436740 max 436740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436740 Ave neighs/atom = 318.32362 Neighbor list builds = 0 Dangerous builds = 0 1372 -4496.06062209466 eV 2.35413487361842 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05