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 = 3.1706996 3.1706996 3.1706996 Created orthogonal box = (0.0000000 -40.356417 0.0000000) to (9.5120988 40.356417 4.4840464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2844993 4.4840464 4.4840464 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -40.356417 0.0000000) to (9.5120988 40.356417 4.4840464) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2844993 4.4840464 4.4840464 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -40.356417 0.0000000) to (9.5120988 40.356417 4.4840464) create_atoms CPU = 0.000 seconds 110 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 3 25 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 216 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_468686727341_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.403 | 4.403 | 4.403 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2316.865 0 -2316.865 7741.0773 32 0 -2332.7865 0 -2332.7865 13571.517 Loop time of 3.44601 on 1 procs for 32 steps with 216 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 = -2316.86501580906 -2332.78520254092 -2332.78648473017 Force two-norm initial, final = 26.905734 0.11039572 Force max component initial, final = 9.2991170 0.017145328 Final line search alpha, max atom move = 1.0000000 0.017145328 Iterations, force evaluations = 32 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.443 | 3.443 | 3.443 | 0.0 | 99.91 Neigh | 0.0012011 | 0.0012011 | 0.0012011 | 0.0 | 0.03 Comm | 0.00089479 | 0.00089479 | 0.00089479 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008788 | | | 0.03 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1873.00 ave 1873 max 1873 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: 13856.0 ave 13856 max 13856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13856 Ave neighs/atom = 64.148148 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.403 | 4.403 | 4.403 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -2332.7865 0 -2332.7865 13571.517 3442.6197 39 0 -2332.9383 0 -2332.9383 -57.759894 3460.4528 Loop time of 0.627169 on 1 procs for 7 steps with 216 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 = -2332.78648473017 -2332.93829713704 -2332.9383483935 Force two-norm initial, final = 58.262612 0.47241078 Force max component initial, final = 52.792155 0.30518354 Final line search alpha, max atom move = 0.0010971702 0.00033483829 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62645 | 0.62645 | 0.62645 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013492 | 0.00013492 | 0.00013492 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005832 | | | 0.09 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1856.00 ave 1856 max 1856 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: 13824.0 ave 13824 max 13824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13824 Ave neighs/atom = 64.000000 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2332.9383 0 -2332.9383 -57.759894 Loop time of 1.48e-06 on 1 procs for 0 steps with 216 atoms 135.1% 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 | | 1.48e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1874.00 ave 1874 max 1874 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: 13808.0 ave 13808 max 13808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13808 Ave neighs/atom = 63.925926 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.541 | 4.541 | 4.541 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 -2332.9383 -2332.9383 9.5036076 81.199883 4.4842419 -57.759894 -57.759894 -141.17269 -85.996601 53.889604 2.539833 158.95192 Loop time of 1.374e-06 on 1 procs for 0 steps with 216 atoms 145.6% 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 | | 1.374e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1874.00 ave 1874 max 1874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6904.00 ave 6904 max 6904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13808.0 ave 13808 max 13808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13808 Ave neighs/atom = 63.925926 Neighbor list builds = 0 Dangerous builds = 0 216 -664.506685286681 eV 2.53983301323819 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04