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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -40.450553 0.0000000) to (20.223254 40.450553 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6625112 5.6625112 4.0446508 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -40.450553 0.0000000) to (20.223254 40.450553 4.0446508) create_atoms CPU = 0.002 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6625112 5.6625112 4.0446508 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -40.450553 0.0000000) to (20.223254 40.450553 4.0446508) create_atoms CPU = 0.001 seconds 201 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 396 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_344724145339_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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1314.6011 0 -1314.6011 6047.3952 59 0 -1326.1209 0 -1326.1209 -4025.4593 Loop time of 5.00086 on 1 procs for 59 steps with 396 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1314.60110526707 -1326.11973217104 -1326.12088128871 Force two-norm initial, final = 12.686875 0.080063718 Force max component initial, final = 3.8613727 0.014540725 Final line search alpha, max atom move = 1.0000000 0.014540725 Iterations, force evaluations = 59 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9733 | 4.9733 | 4.9733 | 0.0 | 99.45 Neigh | 0.011745 | 0.011745 | 0.011745 | 0.0 | 0.23 Comm | 0.0081884 | 0.0081884 | 0.0081884 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007604 | | | 0.15 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3128.00 ave 3128 max 3128 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: 31736.0 ave 31736 max 31736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31736 Ave neighs/atom = 80.141414 Neighbor list builds = 2 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -1326.1209 0 -1326.1209 -4025.4593 6617.387 63 0 -1326.1602 0 -1326.1602 -542.55036 6587.7174 Loop time of 0.338935 on 1 procs for 4 steps with 396 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1326.12088128871 -1326.15934319235 -1326.16016234569 Force two-norm initial, final = 23.048482 0.091738974 Force max component initial, final = 18.581200 0.022584105 Final line search alpha, max atom move = 0.00057343965 1.2950621e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33683 | 0.33683 | 0.33683 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045993 | 0.00045993 | 0.00045993 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00165 | | | 0.49 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3109.00 ave 3109 max 3109 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: 31408.0 ave 31408 max 31408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31408 Ave neighs/atom = 79.313131 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1326.1602 0 -1326.1602 -542.55036 Loop time of 6.435e-06 on 1 procs for 0 steps with 396 atoms 186.5% 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 | | 6.435e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3109.00 ave 3109 max 3109 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: 32348.0 ave 32348 max 32348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32348 Ave neighs/atom = 81.686869 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.582 | 4.582 | 4.582 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 -1326.1602 -1326.1602 20.202455 80.901106 4.0306618 -542.55036 -542.55036 -0.54123014 -1629.1341 2.0242493 2.5545627 192.3175 Loop time of 6.575e-06 on 1 procs for 0 steps with 396 atoms 304.2% 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 | | 6.575e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3109.00 ave 3109 max 3109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16174.0 ave 16174 max 16174 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32348.0 ave 32348 max 32348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32348 Ave neighs/atom = 81.686869 Neighbor list builds = 0 Dangerous builds = 0 396 -1326.16016234569 eV 2.55456267166849 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05