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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -40.848970 0.0000000) to (28.884584 40.848970 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0972795 6.4076816 5.7200000 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.848970 0.0000000) to (28.884584 40.848970 5.7200000) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0972795 6.4076816 5.7200000 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.848970 0.0000000) to (28.884584 40.848970 5.7200000) create_atoms CPU = 0.001 seconds 410 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_616482358807_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2498.7852 0 -2498.7852 34025.226 69 0 -2717.5988 0 -2717.5988 1873.0219 Loop time of 3.53321 on 1 procs for 69 steps with 812 atoms 92.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2498.78517969715 -2717.59646275636 -2717.59879695749 Force two-norm initial, final = 319.93717 0.11374972 Force max component initial, final = 94.673907 0.017693743 Final line search alpha, max atom move = 1.0000000 0.017693743 Iterations, force evaluations = 69 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5135 | 3.5135 | 3.5135 | 0.0 | 99.44 Neigh | 0.0081773 | 0.0081773 | 0.0081773 | 0.0 | 0.23 Comm | 0.0054366 | 0.0054366 | 0.0054366 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006097 | | | 0.17 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3617.00 ave 3617 max 3617 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: 61632.0 ave 61632 max 61632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61632 Ave neighs/atom = 75.901478 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -2717.5988 0 -2717.5988 1873.0219 13498.119 73 0 -2717.6583 0 -2717.6583 -77.068948 13531.912 Loop time of 0.155463 on 1 procs for 4 steps with 812 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 = -2717.59879695749 -2717.65583573542 -2717.65831735669 Force two-norm initial, final = 34.516284 1.1476361 Force max component initial, final = 31.793055 0.72720189 Final line search alpha, max atom move = 0.00023505192 0.00017093020 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15437 | 0.15437 | 0.15437 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020885 | 0.00020885 | 0.00020885 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008845 | | | 0.57 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3969.00 ave 3969 max 3969 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: 61944.0 ave 61944 max 61944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61944 Ave neighs/atom = 76.285714 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.677 | 4.677 | 4.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2717.6583 0 -2717.6583 -77.068948 Loop time of 1.617e-06 on 1 procs for 0 steps with 812 atoms 185.5% 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 | | 1.617e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3969.00 ave 3969 max 3969 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: 61816.0 ave 61816 max 61816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61816 Ave neighs/atom = 76.128079 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.677 | 4.677 | 4.677 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 -2717.6583 -2717.6583 28.895022 82.006191 5.7107021 -77.068948 -77.068948 -86.131716 -65.689083 -79.386046 2.57102 576.10481 Loop time of 1.527e-06 on 1 procs for 0 steps with 812 atoms 196.5% 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 | | 1.527e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3969.00 ave 3969 max 3969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30908.0 ave 30908 max 30908 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61816.0 ave 61816 max 61816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61816 Ave neighs/atom = 76.128079 Neighbor list builds = 0 Dangerous builds = 0 812 -2717.65831735669 eV 2.5710200224072 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04