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 = 3.6149390 3.6149390 3.6149390 Created orthogonal box = (0.0000000 -42.157071 0.0000000) to (14.904775 42.157071 5.1122958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1372605 6.1995693 5.1122958 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.157071 0.0000000) to (14.904775 42.157071 5.1122958) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1372605 6.1995693 5.1122958 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.157071 0.0000000) to (14.904775 42.157071 5.1122958) create_atoms CPU = 0.001 seconds 274 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 4 21 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 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_547744193826_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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.926 | 4.926 | 4.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1857.4888 0 -1857.4888 32167.594 67 0 -1920.3574 0 -1920.3574 12661.352 Loop time of 0.768426 on 1 procs for 67 steps with 544 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 = -1857.48881629224 -1920.35554734317 -1920.35741275479 Force two-norm initial, final = 133.56334 0.13615407 Force max component initial, final = 41.577308 0.021600931 Final line search alpha, max atom move = 1.0000000 0.021600931 Iterations, force evaluations = 67 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75843 | 0.75843 | 0.75843 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0060401 | 0.0060401 | 0.0060401 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003954 | | | 0.51 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5345.00 ave 5345 max 5345 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: 109204.0 ave 109204 max 109204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109204 Ave neighs/atom = 200.74265 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.926 | 4.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1920.3574 0 -1920.3574 12661.352 6424.5371 73 0 -1920.6091 0 -1920.6091 16.93188 6483.4309 Loop time of 0.0515454 on 1 procs for 6 steps with 544 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 = -1920.35741275479 -1920.60904734996 -1920.60910531482 Force two-norm initial, final = 89.110608 0.32342594 Force max component initial, final = 60.441111 0.25788748 Final line search alpha, max atom move = 0.00092828152 0.00023939218 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049504 | 0.049504 | 0.049504 | 0.0 | 96.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036487 | 0.00036487 | 0.00036487 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001676 | | | 3.25 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5325.00 ave 5325 max 5325 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: 109840.0 ave 109840 max 109840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109840 Ave neighs/atom = 201.91176 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1920.6091 0 -1920.6091 16.93188 Loop time of 2.049e-06 on 1 procs for 0 steps with 544 atoms 146.4% 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 | | 2.049e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5325.00 ave 5325 max 5325 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: 109400.0 ave 109400 max 109400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109400 Ave neighs/atom = 201.10294 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 5.064 | 5.064 | 5.064 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 -1920.6091 -1920.6091 14.978424 84.596943 5.1166309 16.93188 16.93188 3.237344 63.942553 -16.384256 2.4199295 368.59792 Loop time of 3.764e-06 on 1 procs for 0 steps with 544 atoms 239.1% 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 | | 3.764e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5325.00 ave 5325 max 5325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54700.0 ave 54700 max 54700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109400.0 ave 109400 max 109400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109400 Ave neighs/atom = 201.10294 Neighbor list builds = 0 Dangerous builds = 0 544 -1920.60910531482 eV 2.41992947850779 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01