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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -71.496103 0.0000000) to (43.782243 71.496103 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0632526 5.1068645 5.8968992 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.496103 0.0000000) to (43.782243 71.496103 8.8453488) create_atoms CPU = 0.004 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0632526 5.1068645 5.8968992 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.496103 0.0000000) to (43.782243 71.496103 8.8453488) create_atoms CPU = 0.003 seconds 2358 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 = 13 43 3 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 6 atoms, new total = 4704 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_260546967793_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 = 13 43 3 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) = 11.40 | 11.40 | 11.40 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18884.224 0 -18884.224 43880.541 120 0 -19914.522 0 -19914.522 5472.5111 Loop time of 61.3954 on 1 procs for 120 steps with 4704 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 = -18884.2237274796 -19914.503725789 -19914.522400059 Force two-norm initial, final = 917.36407 0.67394302 Force max component initial, final = 136.40475 0.098812751 Final line search alpha, max atom move = 0.61658550 0.060926509 Iterations, force evaluations = 120 225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 61.151 | 61.151 | 61.151 | 0.0 | 99.60 Neigh | 0.15641 | 0.15641 | 0.15641 | 0.0 | 0.25 Comm | 0.036382 | 0.036382 | 0.036382 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05141 | | | 0.08 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12697.0 ave 12697 max 12697 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: 603600.0 ave 603600 max 603600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603600 Ave neighs/atom = 128.31633 Neighbor list builds = 4 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 = 13 43 3 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 : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.40 | 11.40 | 11.40 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -19914.522 0 -19914.522 5472.5111 55376.479 125 0 -19915.116 0 -19915.116 -36.178649 55553.308 Loop time of 2.27563 on 1 procs for 5 steps with 4704 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 = -19914.522400059 -19915.1133836176 -19915.1160634767 Force two-norm initial, final = 365.56689 7.4224641 Force max component initial, final = 316.82796 4.5113697 Final line search alpha, max atom move = 3.9409082e-05 0.00017778894 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.269 | 2.269 | 2.269 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084101 | 0.00084101 | 0.00084101 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005746 | | | 0.25 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12696.0 ave 12696 max 12696 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: 605016.0 ave 605016 max 605016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605016 Ave neighs/atom = 128.61735 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 = 13 43 3 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) = 10.91 | 10.91 | 10.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19915.116 0 -19915.116 -36.178649 Loop time of 2.435e-06 on 1 procs for 0 steps with 4704 atoms 164.3% 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 | | 2.435e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12680.0 ave 12680 max 12680 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: 602232.0 ave 602232 max 602232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 602232 Ave neighs/atom = 128.02551 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 = 13 43 3 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) = 10.91 | 10.91 | 10.91 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 -19915.116 -19915.116 43.807967 142.81003 8.8796961 -36.178649 -36.178649 130.1859 -122.93075 -115.7911 2.2111481 2552.6781 Loop time of 2.435e-06 on 1 procs for 0 steps with 4704 atoms 287.5% 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 | | 2.435e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12680.0 ave 12680 max 12680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 301116.0 ave 301116 max 301116 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 602232.0 ave 602232 max 602232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 602232 Ave neighs/atom = 128.02551 Neighbor list builds = 0 Dangerous builds = 0 4704 -19915.1160634767 eV 2.21114806366688 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:05