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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -44.168347 0.0000000) to (9.0158260 44.168347 9.8763426) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4094956 5.8891129 6.5842284 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -44.168347 0.0000000) to (9.0158260 44.168347 9.8763426) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4094956 5.8891129 6.5842284 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.168347 0.0000000) to (9.0158260 44.168347 9.8763426) create_atoms CPU = 0.000 seconds 242 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 20 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1571.3587 0 -1571.3587 15734.026 40 0 -1607.5441 0 -1607.5441 5152.3433 Loop time of 0.36714 on 1 procs for 40 steps with 480 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1571.35872270712 -1607.54275910706 -1607.54411035574 Force two-norm initial, final = 63.298778 0.070277205 Force max component initial, final = 19.871368 0.0074500517 Final line search alpha, max atom move = 1.0000000 0.0074500517 Iterations, force evaluations = 40 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3624 | 0.3624 | 0.3624 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027311 | 0.0027311 | 0.0027311 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002007 | | | 0.55 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4437.00 ave 4437 max 4437 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: 84592.0 ave 84592 max 84592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84592 Ave neighs/atom = 176.23333 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1607.5441 0 -1607.5441 5152.3433 7865.7983 50 0 -1607.7223 0 -1607.7223 -38.427126 7915.8128 Loop time of 0.0688966 on 1 procs for 10 steps with 480 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1607.54411035574 -1607.72231700914 -1607.72233659483 Force two-norm initial, final = 50.168324 0.39211851 Force max component initial, final = 44.789462 0.19965394 Final line search alpha, max atom move = 0.0036417035 0.00072708043 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066023 | 0.066023 | 0.066023 | 0.0 | 95.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049014 | 0.00049014 | 0.00049014 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002383 | | | 3.46 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4107.00 ave 4107 max 4107 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: 84240.0 ave 84240 max 84240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84240 Ave neighs/atom = 175.50000 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.699 | 4.699 | 4.699 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1607.7223 0 -1607.7223 -38.427126 Loop time of 1.733e-06 on 1 procs for 0 steps with 480 atoms 115.4% 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 | | 1.733e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4107.00 ave 4107 max 4107 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: 83996.0 ave 83996 max 83996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83996 Ave neighs/atom = 174.99167 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 4.699 | 4.699 | 4.699 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 -1607.7223 -1607.7223 9.0077453 89.122705 9.8603211 -38.427126 -38.427126 -35.263975 -40.769927 -39.247476 2.5461372 366.22243 Loop time of 2.889e-06 on 1 procs for 0 steps with 480 atoms 173.1% 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 | | 2.889e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4107.00 ave 4107 max 4107 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41998.0 ave 41998 max 41998 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83996.0 ave 83996 max 83996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83996 Ave neighs/atom = 174.99167 Neighbor list builds = 0 Dangerous builds = 0 480 -1607.72233659483 eV 2.54613720434716 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00