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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -43.141536 0.0000000) to (52.837374 43.141536 8.9311464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0385571 5.5467689 5.9540976 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -43.141536 0.0000000) to (52.837374 43.141536 8.9311464) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0385571 5.5467689 5.9540976 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -43.141536 0.0000000) to (52.837374 43.141536 8.9311464) create_atoms CPU = 0.002 seconds 1686 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 20 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3348 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.833 | 7.833 | 7.833 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12369.631 0 -12369.631 33743.546 97 0 -12998.263 0 -12998.263 -1584.6052 Loop time of 3.91913 on 1 procs for 97 steps with 3348 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12369.6306612334 -12998.2502373876 -12998.2630602997 Force two-norm initial, final = 454.41102 0.51395677 Force max component initial, final = 61.307046 0.086156903 Final line search alpha, max atom move = 0.84568598 0.072861685 Iterations, force evaluations = 97 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6857 | 3.6857 | 3.6857 | 0.0 | 94.04 Neigh | 0.17697 | 0.17697 | 0.17697 | 0.0 | 4.52 Comm | 0.024061 | 0.024061 | 0.024061 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0324 | | | 0.83 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12147.0 ave 12147 max 12147 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: 742914.0 ave 742914 max 742914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 742914 Ave neighs/atom = 221.89785 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.831 | 7.831 | 7.831 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -12998.263 0 -12998.263 -1584.6052 40716.837 101 0 -12998.641 0 -12998.641 -62.782649 40679.059 Loop time of 0.166344 on 1 procs for 4 steps with 3348 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 = -12998.2630602996 -12998.640652555 -12998.6412981705 Force two-norm initial, final = 224.13950 2.9189111 Force max component initial, final = 210.72028 2.1528944 Final line search alpha, max atom move = 0.00014855735 0.00031982829 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16141 | 0.16141 | 0.16141 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069092 | 0.00069092 | 0.00069092 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004242 | | | 2.55 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12151.0 ave 12151 max 12151 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: 742826.0 ave 742826 max 742826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 742826 Ave neighs/atom = 221.87157 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.969 | 7.969 | 7.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12998.641 0 -12998.641 -62.782649 Loop time of 2.248e-06 on 1 procs for 0 steps with 3348 atoms 177.9% 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 | | 2.248e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12163.0 ave 12163 max 12163 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: 742870.0 ave 742870 max 742870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 742870 Ave neighs/atom = 221.88471 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.969 | 7.969 | 7.969 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 -12998.641 -12998.641 52.681847 86.430843 8.9339014 -62.782649 -62.782649 -53.746913 -49.781447 -84.819586 2.355409 2353.2324 Loop time of 2.841e-06 on 1 procs for 0 steps with 3348 atoms 281.6% 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 | | 2.841e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12163.0 ave 12163 max 12163 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 371435.0 ave 371435 max 371435 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 742870.0 ave 742870 max 742870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 742870 Ave neighs/atom = 221.88471 Neighbor list builds = 0 Dangerous builds = 0 3348 -12998.6412981705 eV 2.35540902309954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04