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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -53.001607 0.0000000) to (18.738898 53.001607 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8582328 5.8890675 5.1000820 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.001607 0.0000000) to (18.738898 53.001607 5.1000820) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8582328 5.8890675 5.1000820 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.001607 0.0000000) to (18.738898 53.001607 5.1000820) create_atoms CPU = 0.001 seconds 434 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 18 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 866 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.700 | 6.700 | 6.700 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3377.5702 0 -3377.5702 60939.593 111 0 -3618.8798 0 -3618.8798 11013.716 Loop time of 4.95129 on 1 procs for 111 steps with 866 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3377.57018840496 -3618.87622829848 -3618.87979673866 Force two-norm initial, final = 228.18390 0.27360167 Force max component initial, final = 64.604129 0.044460904 Final line search alpha, max atom move = 1.0000000 0.044460904 Iterations, force evaluations = 111 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8655 | 4.8655 | 4.8655 | 0.0 | 98.27 Neigh | 0.046733 | 0.046733 | 0.046733 | 0.0 | 0.94 Comm | 0.026653 | 0.026653 | 0.026653 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01237 | | | 0.25 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13055.0 ave 13055 max 13055 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: 536336.0 ave 536336 max 536336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536336 Ave neighs/atom = 619.32564 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.699 | 6.699 | 6.699 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -3618.8798 0 -3618.8798 11013.716 10130.718 119 0 -3619.2992 0 -3619.2992 -11.64128 10195.023 Loop time of 0.294801 on 1 procs for 8 steps with 866 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 = -3618.87979673867 -3619.29854313434 -3619.29917932365 Force two-norm initial, final = 145.50314 0.72440544 Force max component initial, final = 135.32818 0.38808494 Final line search alpha, max atom move = 0.00020556509 7.9776714e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28874 | 0.28874 | 0.28874 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011521 | 0.0011521 | 0.0011521 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004907 | | | 1.66 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12950.0 ave 12950 max 12950 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: 536392.0 ave 536392 max 536392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536392 Ave neighs/atom = 619.39030 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.837 | 6.837 | 6.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3619.2992 0 -3619.2992 -11.64128 Loop time of 2.072e-06 on 1 procs for 0 steps with 866 atoms 193.1% 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 | | 2.072e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12950.0 ave 12950 max 12950 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: 532716.0 ave 532716 max 532716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 532716 Ave neighs/atom = 615.14550 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.837 | 6.837 | 6.837 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 -3619.2992 -3619.2992 18.72332 106.67557 5.1043493 -11.64128 -11.64128 -11.200322 37.316151 -61.039669 2.3080485 529.36567 Loop time of 2.254e-06 on 1 procs for 0 steps with 866 atoms 221.8% 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 | | 2.254e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12950.0 ave 12950 max 12950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 266358.0 ave 266358 max 266358 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 532716.0 ave 532716 max 532716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 532716 Ave neighs/atom = 615.14550 Neighbor list builds = 0 Dangerous builds = 0 866 -3619.29917932365 eV 2.3080484627934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05