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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -63.736260 0.0000000) to (39.027850 63.736260 9.9130839) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2948146 6.1676335 6.6087226 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -63.736260 0.0000000) to (39.027850 63.736260 9.9130839) create_atoms CPU = 0.002 seconds 1491 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2948146 6.1676335 6.6087226 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -63.736260 0.0000000) to (39.027850 63.736260 9.9130839) create_atoms CPU = 0.002 seconds 1491 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 36 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 2940 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9812.0305 0 -9812.0305 -107.74281 37 0 -9855.9026 0 -9855.9026 -6200.4924 Loop time of 7.5127 on 1 procs for 37 steps with 2940 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 = -9812.03052996123 -9855.89506535596 -9855.90259355193 Force two-norm initial, final = 26.709244 0.25012000 Force max component initial, final = 5.3754754 0.036750667 Final line search alpha, max atom move = 1.0000000 0.036750667 Iterations, force evaluations = 37 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.4799 | 7.4799 | 7.4799 | 0.0 | 99.56 Neigh | 0.019286 | 0.019286 | 0.019286 | 0.0 | 0.26 Comm | 0.0053418 | 0.0053418 | 0.0053418 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00817 | | | 0.11 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7807.00 ave 7807 max 7807 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: 250746.0 ave 250746 max 250746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250746 Ave neighs/atom = 85.287755 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -9855.9026 0 -9855.9026 -6200.4924 49317.379 42 0 -9856.5509 0 -9856.5509 -872.54014 48977.22 Loop time of 0.905853 on 1 procs for 5 steps with 2940 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9855.90259355188 -9856.54928070923 -9856.55093244638 Force two-norm initial, final = 261.44684 0.29699222 Force max component initial, final = 195.36596 0.029534097 Final line search alpha, max atom move = 0.00017237484 5.0909352e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90236 | 0.90236 | 0.90236 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047934 | 0.00047934 | 0.00047934 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003014 | | | 0.33 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827.00 ave 7827 max 7827 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: 250968.0 ave 250968 max 250968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250968 Ave neighs/atom = 85.363265 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.769 | 5.769 | 5.769 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9856.5509 0 -9856.5509 -872.54014 Loop time of 1.81e-06 on 1 procs for 0 steps with 2940 atoms 165.7% 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 | | 1.81e-06 | | |100.00 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827.00 ave 7827 max 7827 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: 251250.0 ave 251250 max 251250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251250 Ave neighs/atom = 85.459184 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.769 | 5.769 | 5.769 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 -9856.5509 -9856.5509 38.919426 127.47252 9.8721362 -872.54014 -872.54014 -0.77026546 -2617.0361 0.18592423 2.4606519 1801.2123 Loop time of 1.926e-06 on 1 procs for 0 steps with 2940 atoms 207.7% 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 | | 1.926e-06 | | |100.00 Nlocal: 2940.00 ave 2940 max 2940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827.00 ave 7827 max 7827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125625.0 ave 125625 max 125625 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 251250.0 ave 251250 max 251250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251250 Ave neighs/atom = 85.459184 Neighbor list builds = 0 Dangerous builds = 0 2940 -9856.55093244638 eV 2.46065185699548 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09