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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -60.197217 0.0000000) to (34.754880 60.197217 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1277691 4.6052516 5.4500000 Created 732 atoms using lattice units in orthogonal box = (0.0000000 -60.197217 0.0000000) to (34.754880 60.197217 5.4500000) create_atoms CPU = 0.002 seconds 732 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1277691 4.6052516 5.4500000 Created 734 atoms using lattice units in orthogonal box = (0.0000000 -60.197217 0.0000000) to (34.754880 60.197217 5.4500000) create_atoms CPU = 0.001 seconds 734 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 36 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1466 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.698 | 4.698 | 4.698 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9261.2117 0 -9261.2117 122469.27 108 0 -9951.649 0 -9951.649 8471.3903 Loop time of 8.96248 on 1 procs for 108 steps with 1466 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9261.21168636169 -9951.63938799218 -9951.64898420475 Force two-norm initial, final = 569.04774 0.52212633 Force max component initial, final = 132.36373 0.10922465 Final line search alpha, max atom move = 0.73522776 0.080304996 Iterations, force evaluations = 108 208 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9225 | 8.9225 | 8.9225 | 0.0 | 99.55 Neigh | 0.0091455 | 0.0091455 | 0.0091455 | 0.0 | 0.10 Comm | 0.015809 | 0.015809 | 0.015809 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01505 | | | 0.17 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6479.00 ave 6479 max 6479 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: 97924.0 ave 97924 max 97924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97924 Ave neighs/atom = 66.796726 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.698 | 4.698 | 4.698 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -9951.649 0 -9951.649 8471.3903 22804.403 111 0 -9951.8775 0 -9951.8775 0.3020873 22877.233 Loop time of 0.248316 on 1 procs for 3 steps with 1466 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 = -9951.64898420481 -9951.86773551276 -9951.8774829121 Force two-norm initial, final = 214.80916 1.4206191 Force max component initial, final = 161.19728 1.0175951 Final line search alpha, max atom move = 4.7413835e-05 4.8248084e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24656 | 0.24656 | 0.24656 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031262 | 0.00031262 | 0.00031262 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001444 | | | 0.58 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6472.00 ave 6472 max 6472 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: 97884.0 ave 97884 max 97884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97884 Ave neighs/atom = 66.769441 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.836 | 4.836 | 4.836 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9951.8775 0 -9951.8775 0.3020873 Loop time of 1.936e-06 on 1 procs for 0 steps with 1466 atoms 155.0% 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 | | 1.936e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6465.00 ave 6465 max 6465 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: 97348.0 ave 97348 max 97348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97348 Ave neighs/atom = 66.403820 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.836 | 4.836 | 4.836 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 -9951.8775 -9951.8775 34.777284 120.66419 5.4516685 0.3020873 0.3020873 71.311852 -13.673716 -56.731874 2.5247297 555.62223 Loop time of 1.798e-06 on 1 procs for 0 steps with 1466 atoms 166.9% 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 | | 1.798e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6465.00 ave 6465 max 6465 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48674.0 ave 48674 max 48674 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97348.0 ave 97348 max 97348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97348 Ave neighs/atom = 66.403820 Neighbor list builds = 0 Dangerous builds = 0 1466 -9951.8774829121 eV 2.52472966742618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09