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 -53.075902 0.0000000) to (37.530330 53.075902 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9823870 6.7887781 5.7233217 Created 685 atoms using lattice units in orthogonal box = (0.0000000 -53.075902 0.0000000) to (37.530330 53.075902 5.7233217) create_atoms CPU = 0.002 seconds 685 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9823870 6.7887781 5.7233217 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -53.075902 0.0000000) to (37.530330 53.075902 5.7233217) create_atoms CPU = 0.001 seconds 693 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 30 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1376 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 30 2 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) = 5.058 | 5.058 | 5.058 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4383.665 0 -4383.665 27669.671 65 0 -4611.1177 0 -4611.1177 3098.107 Loop time of 6.68527 on 1 procs for 65 steps with 1376 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4383.66497423652 -4611.11366637929 -4611.11769483179 Force two-norm initial, final = 279.64589 0.18682192 Force max component initial, final = 41.889832 0.026556473 Final line search alpha, max atom move = 1.0000000 0.026556473 Iterations, force evaluations = 65 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.66 | 6.66 | 6.66 | 0.0 | 99.62 Neigh | 0.008893 | 0.008893 | 0.008893 | 0.0 | 0.13 Comm | 0.0082447 | 0.0082447 | 0.0082447 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008168 | | | 0.12 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6149.00 ave 6149 max 6149 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: 117870.0 ave 117870 max 117870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117870 Ave neighs/atom = 85.661337 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 30 2 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.058 | 5.058 | 5.058 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -4611.1177 0 -4611.1177 3098.107 22801.211 70 0 -4611.2493 0 -4611.2493 -2.1719394 22890.729 Loop time of 0.463345 on 1 procs for 5 steps with 1376 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 = -4611.1176948318 -4611.24710852997 -4611.24930230037 Force two-norm initial, final = 80.826971 0.31286503 Force max component initial, final = 65.490136 0.16877765 Final line search alpha, max atom move = 8.1368160e-05 1.3733127e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46107 | 0.46107 | 0.46107 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037865 | 0.00037865 | 0.00037865 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001892 | | | 0.41 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6149.00 ave 6149 max 6149 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: 117780.0 ave 117780 max 117780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117780 Ave neighs/atom = 85.595930 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 31 2 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) = 5.196 | 5.196 | 5.196 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4611.2493 0 -4611.2493 -2.1719394 Loop time of 1.715e-06 on 1 procs for 0 steps with 1376 atoms 174.9% 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 | | 1.715e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6149.00 ave 6149 max 6149 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: 117666.0 ave 117666 max 117666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117666 Ave neighs/atom = 85.513081 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 31 2 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) = 5.196 | 5.196 | 5.196 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 -4611.2493 -4611.2493 37.512971 106.58691 5.7249843 -2.1719394 -2.1719394 -11.807685 -4.0354908 9.3273576 2.6703382 884.60564 Loop time of 1.998e-06 on 1 procs for 0 steps with 1376 atoms 150.2% 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 | | 1.998e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6149.00 ave 6149 max 6149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58833.0 ave 58833 max 58833 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117666.0 ave 117666 max 117666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117666 Ave neighs/atom = 85.513081 Neighbor list builds = 0 Dangerous builds = 0 1376 -4611.24930230037 eV 2.67033820970141 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07