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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -64.113442 0.0000000) to (39.258812 64.113442 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3320664 6.2041327 6.6478321 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -64.113442 0.0000000) to (39.258812 64.113442 9.9717481) create_atoms CPU = 0.002 seconds 1492 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3320664 6.2041327 6.6478321 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -64.113442 0.0000000) to (39.258812 64.113442 9.9717481) create_atoms CPU = 0.002 seconds 1492 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 43 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2952 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 43 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.161 | 5.161 | 5.161 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9870.6938 0 -9870.6938 2137.6756 77 0 -9918.0375 0 -9918.0375 -4425.7726 Loop time of 10.115 on 1 procs for 77 steps with 2952 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 = -9870.69384478057 -9918.02845536195 -9918.03752740623 Force two-norm initial, final = 35.105230 0.26343651 Force max component initial, final = 6.7672176 0.024640027 Final line search alpha, max atom move = 1.0000000 0.024640027 Iterations, force evaluations = 77 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.091 | 10.091 | 10.091 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0082957 | 0.0082957 | 0.0082957 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01588 | | | 0.16 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6575.00 ave 6575 max 6575 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: 158264.0 ave 158264 max 158264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158264 Ave neighs/atom = 53.612466 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 43 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.159 | 5.159 | 5.159 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -9918.0375 0 -9918.0375 -4425.7726 50198.129 80 0 -9918.2733 0 -9918.2733 -870.20472 50016.536 Loop time of 0.435875 on 1 procs for 3 steps with 2952 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 = -9918.03752740621 -9918.27273810168 -9918.27328799973 Force two-norm initial, final = 186.18223 0.34937632 Force max component initial, final = 136.19288 0.11520806 Final line search alpha, max atom move = 0.00026824108 3.0903534e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43366 | 0.43366 | 0.43366 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028511 | 0.00028511 | 0.00028511 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001928 | | | 0.44 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6227.00 ave 6227 max 6227 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: 158774.0 ave 158774 max 158774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158774 Ave neighs/atom = 53.785230 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 43 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.297 | 5.297 | 5.297 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9918.2733 0 -9918.2733 -870.20472 Loop time of 1.801e-06 on 1 procs for 0 steps with 2952 atoms 166.6% 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 | | 1.801e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6252.00 ave 6252 max 6252 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: 158782.0 ave 158782 max 158782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158782 Ave neighs/atom = 53.787940 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 43 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.297 | 5.297 | 5.297 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 -9918.2733 -9918.2733 39.197489 128.22688 9.9512188 -870.20472 -870.20472 3.3847452 -2617.6818 3.6828546 2.537893 1333.4908 Loop time of 2.199e-06 on 1 procs for 0 steps with 2952 atoms 181.9% 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 | | 2.199e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6252.00 ave 6252 max 6252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79391.0 ave 79391 max 79391 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158782.0 ave 158782 max 158782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158782 Ave neighs/atom = 53.787940 Neighbor list builds = 0 Dangerous builds = 0 2952 -9918.27328799973 eV 2.53789302810654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11