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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -34.990462 0.0000000) to (17.493482 34.990462 3.4986963) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8981749 4.8981749 3.4986963 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -34.990462 0.0000000) to (17.493482 34.990462 3.4986963) create_atoms CPU = 0.001 seconds 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8981749 4.8981749 3.4986963 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -34.990462 0.0000000) to (17.493482 34.990462 3.4986963) create_atoms CPU = 0.000 seconds 202 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 = 5 19 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 399 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 = 5 19 1 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) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1607.2189 0 -1607.2189 25286.413 86 0 -1636.2682 0 -1636.2682 -291.24515 Loop time of 1.11987 on 1 procs for 86 steps with 399 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1607.21890241981 -1636.26664570359 -1636.26819614136 Force two-norm initial, final = 31.572932 0.16452348 Force max component initial, final = 10.886408 0.055163963 Final line search alpha, max atom move = 1.0000000 0.055163963 Iterations, force evaluations = 86 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0999 | 1.0999 | 1.0999 | 0.0 | 98.21 Neigh | 0.0040486 | 0.0040486 | 0.0040486 | 0.0 | 0.36 Comm | 0.0092916 | 0.0092916 | 0.0092916 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006677 | | | 0.60 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4121.00 ave 4121 max 4121 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: 69526.0 ave 69526 max 69526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69526 Ave neighs/atom = 174.25063 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 19 1 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 : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -1636.2682 0 -1636.2682 -291.24515 4283.1391 96 0 -1636.4432 0 -1636.4432 -3765.1652 4295.4395 Loop time of 0.0929293 on 1 procs for 10 steps with 399 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 = -1636.26819614136 -1636.44298332826 -1636.44322032057 Force two-norm initial, final = 29.520716 0.61707215 Force max component initial, final = 24.654332 0.22334473 Final line search alpha, max atom move = 0.0013997497 0.00031262672 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08922 | 0.08922 | 0.08922 | 0.0 | 96.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069343 | 0.00069343 | 0.00069343 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003016 | | | 3.25 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4126.00 ave 4126 max 4126 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: 69716.0 ave 69716 max 69716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69716 Ave neighs/atom = 174.72682 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 = 5 19 1 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) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1636.4432 0 -1636.4432 -3765.1652 Loop time of 2.157e-06 on 1 procs for 0 steps with 399 atoms 185.4% 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 | | 2.157e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4136.00 ave 4136 max 4136 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: 69686.0 ave 69686 max 69686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69686 Ave neighs/atom = 174.65163 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 = 5 19 1 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) = 4.614 | 4.614 | 4.614 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 -1636.4432 -1636.4432 17.381887 69.980924 3.5312707 -3765.1652 -3765.1652 75.206406 -11286.62 -84.082037 2.2405847 128.93682 Loop time of 1.816e-06 on 1 procs for 0 steps with 399 atoms 220.3% 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 | | 1.816e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4136.00 ave 4136 max 4136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34843.0 ave 34843 max 34843 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69686.0 ave 69686 max 69686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69686 Ave neighs/atom = 174.65163 Neighbor list builds = 0 Dangerous builds = 0 399 -1636.44322032057 eV 2.24058471606354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01