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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -33.563399 0.0000000) to (23.732907 33.563399 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4127682 5.2994840 4.4455807 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -33.563399 0.0000000) to (23.732907 33.563399 4.4455807) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4127682 5.2994840 4.4455807 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -33.563399 0.0000000) to (23.732907 33.563399 4.4455807) create_atoms CPU = 0.001 seconds 230 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 14 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.899 | 4.899 | 4.899 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2297.21 0 -2297.21 204335.04 85 0 -3002.1261 0 -3002.1261 -10059.546 Loop time of 0.736353 on 1 procs for 85 steps with 452 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 = -2297.20996569166 -3002.12328851556 -3002.12606359715 Force two-norm initial, final = 1407.4565 0.32695064 Force max component initial, final = 488.16822 0.062961944 Final line search alpha, max atom move = 0.66019481 0.041567149 Iterations, force evaluations = 85 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7071 | 0.7071 | 0.7071 | 0.0 | 96.03 Neigh | 0.019766 | 0.019766 | 0.019766 | 0.0 | 2.68 Comm | 0.0060442 | 0.0060442 | 0.0060442 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003438 | | | 0.47 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5504.00 ave 5504 max 5504 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: 124612.0 ave 124612 max 124612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124612 Ave neighs/atom = 275.69027 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.899 | 4.899 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -3002.1261 0 -3002.1261 -10059.546 7082.317 94 0 -3002.9889 0 -3002.9889 -62.201131 7056.3112 Loop time of 0.0573621 on 1 procs for 9 steps with 452 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 = -3002.12606359714 -3002.98807343909 -3002.98886472231 Force two-norm initial, final = 191.15061 1.3551617 Force max component initial, final = 171.87660 0.63438341 Final line search alpha, max atom move = 0.00027098376 0.00017190760 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055131 | 0.055131 | 0.055131 | 0.0 | 96.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048 | 0.00048 | 0.00048 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001751 | | | 3.05 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5504.00 ave 5504 max 5504 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: 124616.0 ave 124616 max 124616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124616 Ave neighs/atom = 275.69912 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3002.9889 0 -3002.9889 -62.201131 Loop time of 1.531e-06 on 1 procs for 0 steps with 452 atoms 130.6% 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 | | 1.531e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5504.00 ave 5504 max 5504 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: 124592.0 ave 124592 max 124592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124592 Ave neighs/atom = 275.64602 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.037 | 5.037 | 5.037 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 -3002.9889 -3002.9889 23.834576 67.146646 4.4090596 -62.201131 -62.201131 2.2401764 -144.08303 -44.760534 2.5622492 504.97547 Loop time of 1.852e-06 on 1 procs for 0 steps with 452 atoms 162.0% 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 | | 1.852e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5504.00 ave 5504 max 5504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62296.0 ave 62296 max 62296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124592.0 ave 124592 max 124592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124592 Ave neighs/atom = 275.64602 Neighbor list builds = 0 Dangerous builds = 0 452 -3002.98886472231 eV 2.56224923676999 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01