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 = 4.0499990 4.0499990 4.0499990 Created orthogonal box = (0.0000000 -58.968876 0.0000000) to (29.484438 58.968876 4.0499990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0067913 5.0067913 4.0499990 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -58.968876 0.0000000) to (29.484438 58.968876 4.0499990) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0067913 5.0067913 4.0499990 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -58.968876 0.0000000) to (29.484438 58.968876 4.0499990) create_atoms CPU = 0.001 seconds 426 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 ghost atom cutoff = 8 binsize = 4, bins = 8 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_093637366498_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.952 | 4.952 | 4.952 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2566.3686 0 -2566.3686 38177.504 62 0 -2839.7588 0 -2839.7588 3896.2478 Loop time of 7.85289 on 1 procs for 62 steps with 848 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2566.36858370877 -2839.75679274632 -2839.75883512452 Force two-norm initial, final = 303.54635 0.11047594 Force max component initial, final = 74.878998 0.027678526 Final line search alpha, max atom move = 1.0000000 0.027678526 Iterations, force evaluations = 62 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8219 | 7.8219 | 7.8219 | 0.0 | 99.60 Neigh | 0.014293 | 0.014293 | 0.014293 | 0.0 | 0.18 Comm | 0.0088847 | 0.0088847 | 0.0088847 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007854 | | | 0.10 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5822.00 ave 5822 max 5822 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: 112700.0 ave 112700 max 112700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112700 Ave neighs/atom = 132.90094 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -2839.7588 0 -2839.7588 3896.2478 14083.176 71 0 -2840.0201 0 -2840.0201 39.453407 14150.184 Loop time of 0.832888 on 1 procs for 9 steps with 848 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2839.75883512452 -2840.01928056277 -2840.02006162092 Force two-norm initial, final = 73.184233 0.67098581 Force max component initial, final = 68.924227 0.36427441 Final line search alpha, max atom move = 0.00047333487 0.00017242378 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82185 | 0.82185 | 0.82185 | 0.0 | 98.67 Neigh | 0.0074567 | 0.0074567 | 0.0074567 | 0.0 | 0.90 Comm | 0.00068695 | 0.00068695 | 0.00068695 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002892 | | | 0.35 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5809.00 ave 5809 max 5809 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: 112680.0 ave 112680 max 112680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112680 Ave neighs/atom = 132.87736 Neighbor list builds = 1 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 ghost atom cutoff = 8 binsize = 4, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2840.0201 0 -2840.0201 39.453407 Loop time of 4.167e-06 on 1 procs for 0 steps with 848 atoms 216.0% 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 | | 4.167e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5809.00 ave 5809 max 5809 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: 112688.0 ave 112688 max 112688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112688 Ave neighs/atom = 132.88679 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 ghost atom cutoff = 8 binsize = 4, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.092 | 5.092 | 5.092 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 -2840.0201 -2840.0201 29.45694 118.93177 4.0390253 39.453407 39.453407 41.207067 39.875381 37.277772 2.6090188 447.66046 Loop time of 2.252e-06 on 1 procs for 0 steps with 848 atoms 222.0% 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 | | 2.252e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5809.00 ave 5809 max 5809 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56344.0 ave 56344 max 56344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112688.0 ave 112688 max 112688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112688 Ave neighs/atom = 132.88679 Neighbor list builds = 0 Dangerous builds = 0 848 -2840.02006162092 eV 2.60901882921431 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09