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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9374714 4.9800000 5.7504086 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) create_atoms CPU = 0.004 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9374714 4.9800000 5.7504086 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 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 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_912636107108_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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.255 | 6.255 | 6.255 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20154.127 0 -20154.127 40365.127 67 0 -20860.072 0 -20860.072 9321.0997 Loop time of 20.2765 on 1 procs for 67 steps with 4704 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 = -20154.127024431 -20860.0537421565 -20860.0719619004 Force two-norm initial, final = 615.22338 0.65142813 Force max component initial, final = 104.96015 0.12001631 Final line search alpha, max atom move = 1.0000000 0.12001631 Iterations, force evaluations = 67 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.219 | 20.219 | 20.219 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02177 | 0.02177 | 0.02177 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03588 | | | 0.18 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11075.0 ave 11075 max 11075 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: 367788.0 ave 367788 max 367788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367788 Ave neighs/atom = 78.186224 Neighbor list builds = 0 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.255 | 6.255 | 6.255 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -20860.072 0 -20860.072 9321.0997 51351.171 74 0 -20861.698 0 -20861.698 -143.77056 51609.382 Loop time of 1.41868 on 1 procs for 7 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 = -20860.0719619004 -20861.696381735 -20861.6978734736 Force two-norm initial, final = 612.96549 10.424276 Force max component initial, final = 562.01718 9.7492905 Final line search alpha, max atom move = 7.5078691e-05 0.00073196397 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4106 | 1.4106 | 1.4106 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093544 | 0.00093544 | 0.00093544 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007138 | | | 0.50 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11130.0 ave 11130 max 11130 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: 366312.0 ave 366312 max 366312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366312 Ave neighs/atom = 77.872449 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.393 | 6.393 | 6.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20861.698 0 -20861.698 -143.77056 Loop time of 2.366e-06 on 1 procs for 0 steps with 4704 atoms 211.3% 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 | | 2.366e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11130.0 ave 11130 max 11130 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: 366048.0 ave 366048 max 366048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366048 Ave neighs/atom = 77.816327 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.393 | 6.393 | 6.393 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 -20861.698 -20861.698 42.680248 140.29447 8.6190854 -143.77056 -143.77056 -302.558 -21.860119 -106.89356 2.2010641 1708.6482 Loop time of 2.744e-06 on 1 procs for 0 steps with 4704 atoms 291.5% 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 | | 2.744e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11130.0 ave 11130 max 11130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183024.0 ave 183024 max 183024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366048.0 ave 366048 max 366048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366048 Ave neighs/atom = 77.816327 Neighbor list builds = 0 Dangerous builds = 0 4704 -20861.6978734736 eV 2.20106407258658 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22