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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -40.787212 0.0000000) to (23.546691 40.787212 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0457195 4.8552459 5.4500000 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -40.787212 0.0000000) to (23.546691 40.787212 5.4500000) create_atoms CPU = 0.003 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0457195 4.8552459 5.4500000 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -40.787212 0.0000000) to (23.546691 40.787212 5.4500000) create_atoms CPU = 0.002 seconds 339 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 = 8 ghost atom cutoff = 8 binsize = 4, 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 672 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_380272712420_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4152.2896 0 -4152.2896 166011.58 83 0 -4546.9668 0 -4546.9668 9795.4252 Loop time of 18.0535 on 1 procs for 83 steps with 672 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 = -4152.28956240676 -4546.96237456618 -4546.96678735709 Force two-norm initial, final = 400.77314 0.37350147 Force max component initial, final = 71.472359 0.093045759 Final line search alpha, max atom move = 1.0000000 0.093045759 Iterations, force evaluations = 83 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.003 | 18.003 | 18.003 | 0.0 | 99.72 Neigh | 0.015002 | 0.015002 | 0.015002 | 0.0 | 0.08 Comm | 0.019128 | 0.019128 | 0.019128 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01635 | | | 0.09 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4707.00 ave 4707 max 4707 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: 91632.0 ave 91632 max 91632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91632 Ave neighs/atom = 136.35714 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4546.9668 0 -4546.9668 9795.4252 10468.402 86 0 -4547.0392 0 -4547.0392 2664.3243 10496.635 Loop time of 0.643636 on 1 procs for 3 steps with 672 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4546.96678735709 -4547.03900864167 -4547.0391620964 Force two-norm initial, final = 75.695309 0.39504883 Force max component initial, final = 56.013191 0.098142188 Final line search alpha, max atom move = 0.00064827703 6.3623327e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64112 | 0.64112 | 0.64112 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057746 | 0.00057746 | 0.00057746 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001937 | | | 0.30 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4660.00 ave 4660 max 4660 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: 91708.0 ave 91708 max 91708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91708 Ave neighs/atom = 136.47024 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.676 | 4.676 | 4.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4547.0392 0 -4547.0392 2664.3243 Loop time of 6.425e-06 on 1 procs for 0 steps with 672 atoms 186.8% 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 | | 6.425e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4646.00 ave 4646 max 4646 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: 91662.0 ave 91662 max 91662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91662 Ave neighs/atom = 136.40179 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.676 | 4.676 | 4.676 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 -4547.0392 -4547.0392 23.573664 81.574424 5.4584457 2664.3243 2664.3243 2.9145393 8002.79 -12.731606 2.5368218 628.99668 Loop time of 8.58e-06 on 1 procs for 0 steps with 672 atoms 268.1% 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 | | 8.58e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4646.00 ave 4646 max 4646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45831.0 ave 45831 max 45831 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91662.0 ave 91662 max 91662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91662 Ave neighs/atom = 136.40179 Neighbor list builds = 0 Dangerous builds = 0 672 -4547.0391620964 eV 2.5368217543959 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19