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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897098 62.179117 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226304 5.5798613 6.0968189 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897098 62.179117 6.0968189) create_atoms CPU = 0.002 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226304 5.5798613 6.0968189 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897098 62.179117 6.0968189) create_atoms CPU = 0.002 seconds 1250 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2478 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10949.296 0 -10949.296 5305.4388 43 0 -10989.19 0 -10989.19 -5033.0861 Loop time of 2.03512 on 1 procs for 43 steps with 2478 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 = -10949.2959558561 -10989.1797808654 -10989.1898198811 Force two-norm initial, final = 63.964184 0.33206064 Force max component initial, final = 10.240991 0.064414632 Final line search alpha, max atom move = 0.97810250 0.063004113 Iterations, force evaluations = 43 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9791 | 1.9791 | 1.9791 | 0.0 | 97.25 Neigh | 0.031177 | 0.031177 | 0.031177 | 0.0 | 1.53 Comm | 0.013296 | 0.013296 | 0.013296 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01153 | | | 0.57 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12663.0 ave 12663 max 12663 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: 553864.0 ave 553864 max 553864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 553864 Ave neighs/atom = 223.51251 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.945 | 6.945 | 6.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -10989.19 0 -10989.19 -5033.0861 27216.807 45 0 -10989.255 0 -10989.255 -1841.8614 27167.998 Loop time of 0.102798 on 1 procs for 2 steps with 2478 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 = -10989.1898198811 -10989.2517375066 -10989.2551036433 Force two-norm initial, final = 94.753591 5.6595597 Force max component initial, final = 85.676536 5.6411896 Final line search alpha, max atom move = 5.1263115e-05 0.00028918495 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10067 | 0.10067 | 0.10067 | 0.0 | 97.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039547 | 0.00039547 | 0.00039547 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001729 | | | 1.68 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12666.0 ave 12666 max 12666 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: 554342.0 ave 554342 max 554342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554342 Ave neighs/atom = 223.70541 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.083 | 7.083 | 7.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10989.255 0 -10989.255 -1841.8614 Loop time of 2.184e-06 on 1 procs for 0 steps with 2478 atoms 228.9% 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 | | 2.184e-06 | | |100.00 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12666.0 ave 12666 max 12666 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: 554418.0 ave 554418 max 554418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554418 Ave neighs/atom = 223.73608 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.083 | 7.083 | 7.083 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 -10989.255 -10989.255 35.8809 124.35823 6.0886325 -1841.8614 -1841.8614 332.52738 -5876.1042 17.992526 2.2001403 931.92258 Loop time of 2.579e-06 on 1 procs for 0 steps with 2478 atoms 310.2% 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 | | 2.579e-06 | | |100.00 Nlocal: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12666.0 ave 12666 max 12666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 277209.0 ave 277209 max 277209 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 554418.0 ave 554418 max 554418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554418 Ave neighs/atom = 223.73608 Neighbor list builds = 0 Dangerous builds = 0 2478 -10921.7759016041 eV 2.2001402656877 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02