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 -37.230588 0.0000000) to (45.597971 37.230588 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2111967 4.7867898 5.1383093 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -37.230588 0.0000000) to (45.597971 37.230588 7.7074639) create_atoms CPU = 0.002 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2111967 4.7867898 5.1383093 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -37.230588 0.0000000) to (45.597971 37.230588 7.7074639) create_atoms CPU = 0.001 seconds 841 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1669 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_805823015127_000#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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.617 | 4.617 | 4.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11104.058 0 -11104.058 27678.708 20 0 -15129.642 0 -15129.642 20063.845 Loop time of 5.06242 on 1 procs for 20 steps with 1669 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 = -11104.0576747182 -15129.6373221177 -15129.6416094778 Force two-norm initial, final = 60.536004 16167.314 Force max component initial, final = 8.2125734 4567.5106 Final line search alpha, max atom move = 2.1243815e-08 9.7031348e-05 Iterations, force evaluations = 20 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0475 | 5.0475 | 5.0475 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0063235 | 0.0063235 | 0.0063235 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008589 | | | 0.17 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4368.00 ave 4368 max 4368 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: 95656.0 ave 95656 max 95656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95656 Ave neighs/atom = 57.313361 Neighbor list builds = 0 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.617 | 4.617 | 4.617 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -15129.642 0 -15129.642 20063.845 26168.987 32 0 -16647.126 0 -16647.126 7510.6479 26279.397 Loop time of 4.07015 on 1 procs for 12 steps with 1669 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15129.6416094779 -16647.1203559606 -16647.1257214879 Force two-norm initial, final = 16179.016 922.71465 Force max component initial, final = 4567.5106 403.14404 Final line search alpha, max atom move = 4.0416343e-08 1.6293608e-05 Iterations, force evaluations = 12 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0379 | 4.0379 | 4.0379 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041388 | 0.0041388 | 0.0041388 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02815 | | | 0.69 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4367.00 ave 4367 max 4367 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: 95688.0 ave 95688 max 95688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95688 Ave neighs/atom = 57.332534 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.755 | 4.755 | 4.755 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16647.126 0 -16647.126 7510.6479 Loop time of 3.91e-06 on 1 procs for 0 steps with 1669 atoms 230.2% 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 | | 3.91e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4367.00 ave 4367 max 4367 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: 95644.0 ave 95644 max 95644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95644 Ave neighs/atom = 57.306171 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.755 | 4.755 | 4.755 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 -16647.126 -16647.126 45.639883 74.596598 7.7188368 7510.6479 7510.6479 2061.89 11720.203 8749.8511 0.0056859154 1935.4577 Loop time of 2.452e-06 on 1 procs for 0 steps with 1669 atoms 203.9% 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 | | 2.452e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4367.00 ave 4367 max 4367 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47822.0 ave 47822 max 47822 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95644.0 ave 95644 max 95644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95644 Ave neighs/atom = 57.306171 Neighbor list builds = 0 Dangerous builds = 0 1669 -16647.1257214879 eV 0.00568591537660846 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09