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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -35.889894 0.0000000) to (31.081560 35.889894 6.0955954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5787415 5.5215222 6.0955954 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -35.889894 0.0000000) to (31.081560 35.889894 6.0955954) create_atoms CPU = 0.004 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5787415 5.5215222 6.0955954 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.889894 0.0000000) to (31.081560 35.889894 6.0955954) create_atoms CPU = 0.004 seconds 628 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1250 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.448 | 5.448 | 5.448 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4542.4216 0 -4542.4216 206020.48 116 0 -5526.9423 0 -5526.9423 15240.034 Loop time of 5.27589 on 1 procs for 116 steps with 1250 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 = -4542.42157249287 -5526.93745066302 -5526.9423180792 Force two-norm initial, final = 2271.6301 0.25115252 Force max component initial, final = 552.38693 0.051142258 Final line search alpha, max atom move = 1.0000000 0.051142258 Iterations, force evaluations = 116 207 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0932 | 5.0932 | 5.0932 | 0.0 | 96.54 Neigh | 0.11616 | 0.11616 | 0.11616 | 0.0 | 2.20 Comm | 0.034361 | 0.034361 | 0.034361 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03216 | | | 0.61 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6240.00 ave 6240 max 6240 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: 217176.0 ave 217176 max 217176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217176 Ave neighs/atom = 173.74080 Neighbor list builds = 4 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.448 | 5.448 | 5.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -5526.9423 0 -5526.9423 15240.034 13599.443 126 0 -5528.0245 0 -5528.0245 -89.442752 13719.455 Loop time of 0.295874 on 1 procs for 10 steps with 1250 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 = -5526.94231807914 -5528.02430820441 -5528.02448413282 Force two-norm initial, final = 261.50490 1.6435048 Force max component initial, final = 235.95068 1.2255454 Final line search alpha, max atom move = 0.00052696114 0.00064581479 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28786 | 0.28786 | 0.28786 | 0.0 | 97.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016478 | 0.0016478 | 0.0016478 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00637 | | | 2.15 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6245.00 ave 6245 max 6245 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: 217308.0 ave 217308 max 217308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217308 Ave neighs/atom = 173.84640 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.586 | 5.586 | 5.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5528.0245 0 -5528.0245 -89.442752 Loop time of 6.365e-06 on 1 procs for 0 steps with 1250 atoms 204.2% 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 | | 6.365e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6239.00 ave 6239 max 6239 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: 216864.0 ave 216864 max 216864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216864 Ave neighs/atom = 173.49120 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.586 | 5.586 | 5.586 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 -5528.0245 -5528.0245 31.103023 72.43096 6.0898979 -89.442752 -89.442752 -143.21968 -49.622576 -75.486004 2.1702813 805.10362 Loop time of 6.726e-06 on 1 procs for 0 steps with 1250 atoms 267.6% 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 | | 6.726e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6239.00 ave 6239 max 6239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108432.0 ave 108432 max 108432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216864.0 ave 216864 max 216864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216864 Ave neighs/atom = 173.49120 Neighbor list builds = 0 Dangerous builds = 0 1250 -5528.02448413283 eV 2.17028128960441 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06