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 = 3.1692585 3.1692585 3.1692585 Created orthogonal box = (0.0000000 -58.438239 0.0000000) to (29.219119 58.438239 3.1692585) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4688065 4.4688065 3.1692585 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -58.438239 0.0000000) to (29.219119 58.438239 3.1692585) create_atoms CPU = 0.001 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4688065 4.4688065 3.1692585 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.438239 0.0000000) to (29.219119 58.438239 3.1692585) create_atoms CPU = 0.000 seconds 341 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 36 1 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 681 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_014123846623_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7305.1947 0 -7305.1947 26360.598 41 0 -7376.0728 0 -7376.0728 6836.2105 Loop time of 15.186 on 1 procs for 41 steps with 681 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 = -7305.19466422763 -7376.06668437566 -7376.07281155294 Force two-norm initial, final = 85.605273 0.28009386 Force max component initial, final = 23.820245 0.050665518 Final line search alpha, max atom move = 1.0000000 0.050665518 Iterations, force evaluations = 41 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.176 | 15.176 | 15.176 | 0.0 | 99.93 Neigh | 0.0038083 | 0.0038083 | 0.0038083 | 0.0 | 0.03 Comm | 0.0035218 | 0.0035218 | 0.0035218 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003174 | | | 0.02 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4868.00 ave 4868 max 4868 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: 43768.0 ave 43768 max 43768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43768 Ave neighs/atom = 64.270191 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -7376.0728 0 -7376.0728 6836.2105 10823.106 45 0 -7376.2032 0 -7376.2032 -216.78063 10852.57 Loop time of 1.19736 on 1 procs for 4 steps with 681 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 = -7376.07281155294 -7376.20248631992 -7376.20322539743 Force two-norm initial, final = 93.148680 3.8371039 Force max component initial, final = 83.998669 3.5514734 Final line search alpha, max atom move = 0.00015797127 0.00056103076 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1962 | 1.1962 | 1.1962 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021098 | 0.00021098 | 0.00021098 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009046 | | | 0.08 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4926.00 ave 4926 max 4926 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: 43776.0 ave 43776 max 43776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43776 Ave neighs/atom = 64.281938 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7376.2032 0 -7376.2032 -216.78063 Loop time of 1.989e-06 on 1 procs for 0 steps with 681 atoms 150.8% 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 | | 1.989e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4926.00 ave 4926 max 4926 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: 43752.0 ave 43752 max 43752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43752 Ave neighs/atom = 64.246696 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.666 | 4.666 | 4.666 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 -7376.2032 -7376.2032 29.220562 117.24778 3.1676662 -216.78063 -216.78063 -524.33371 71.625301 -197.63348 2.5005998 126.58172 Loop time of 7.582e-06 on 1 procs for 0 steps with 681 atoms 145.1% 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 | | 7.582e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4926.00 ave 4926 max 4926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21876.0 ave 21876 max 21876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43752.0 ave 43752 max 43752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43752 Ave neighs/atom = 64.246696 Neighbor list builds = 0 Dangerous builds = 0 681 -3729.71674808995 eV 2.50059982691831 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17