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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -36.584036 0.0000000) to (18.292018 36.584036 3.6584036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1217650 5.1217650 3.6584036 Created 199 atoms using lattice units in orthogonal box = (0.0000000 -36.584036 0.0000000) to (18.292018 36.584036 3.6584036) create_atoms CPU = 0.001 seconds 199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1217650 5.1217650 3.6584036 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.584036 0.0000000) to (18.292018 36.584036 3.6584036) 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 400 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1524.1296 0 -1524.1296 24849.388 167 0 -1555.3527 0 -1555.3527 -6755.5136 Loop time of 2.21692 on 1 procs for 167 steps with 400 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 = -1524.12957908374 -1555.35136838963 -1555.35266633486 Force two-norm initial, final = 41.409374 0.10575367 Force max component initial, final = 13.367994 0.032231638 Final line search alpha, max atom move = 1.0000000 0.032231638 Iterations, force evaluations = 167 314 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1514 | 2.1514 | 2.1514 | 0.0 | 97.04 Neigh | 0.014392 | 0.014392 | 0.014392 | 0.0 | 0.65 Comm | 0.028562 | 0.028562 | 0.028562 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02258 | | | 1.02 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3960.00 ave 3960 max 3960 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: 55110.0 ave 55110 max 55110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55110 Ave neighs/atom = 137.77500 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 167 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 167 0 -1555.3527 0 -1555.3527 -6755.5136 4896.377 261 0 -1564.3451 0 -1564.3451 462.93354 4848.6779 Loop time of 0.782992 on 1 procs for 94 steps with 400 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 = -1555.35266633486 -1564.34404836443 -1564.34507246582 Force two-norm initial, final = 214.64569 3.1790949 Force max component initial, final = 148.17524 1.5343720 Final line search alpha, max atom move = 0.00049560356 0.00076044022 Iterations, force evaluations = 94 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7159 | 0.7159 | 0.7159 | 0.0 | 91.43 Neigh | 0.027538 | 0.027538 | 0.027538 | 0.0 | 3.52 Comm | 0.0092135 | 0.0092135 | 0.0092135 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03034 | | | 3.88 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4005.00 ave 4005 max 4005 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: 56826.0 ave 56826 max 56826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56826 Ave neighs/atom = 142.06500 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1564.3451 0 -1564.3451 462.93354 Loop time of 6.345e-06 on 1 procs for 0 steps with 400 atoms 173.4% 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 | | 6.345e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4020.00 ave 4020 max 4020 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: 57118.0 ave 57118 max 57118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57118 Ave neighs/atom = 142.79500 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.594 | 4.594 | 4.594 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 -1564.3451 -1564.3451 18.083784 69.371693 3.8650197 462.93354 462.93354 409.78377 443.37094 535.6459 2.2301159 188.10513 Loop time of 6.676e-06 on 1 procs for 0 steps with 400 atoms 254.6% 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 | | 6.676e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4020.00 ave 4020 max 4020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28559.0 ave 28559 max 28559 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57118.0 ave 57118 max 57118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57118 Ave neighs/atom = 142.79500 Neighbor list builds = 0 Dangerous builds = 0 400 -1564.34507246582 eV 2.23011591609948 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04