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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -54.976656 0.0000000) to (27.486568 54.976656 3.5192945) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9565943 4.9565943 3.5192945 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.976656 0.0000000) to (27.486568 54.976656 3.5192945) create_atoms CPU = 0.001 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9565943 4.9565943 3.5192945 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.976656 0.0000000) to (27.486568 54.976656 3.5192945) create_atoms CPU = 0.001 seconds 490 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 29 1 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4277.1429 0 -4277.1429 26696.297 119 0 -4324.1442 0 -4324.1442 -1351.0571 Loop time of 1.93063 on 1 procs for 119 steps with 974 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 = -4277.14285561649 -4324.14060336747 -4324.14420466454 Force two-norm initial, final = 49.274569 0.21475537 Force max component initial, final = 15.670572 0.021066655 Final line search alpha, max atom move = 1.0000000 0.021066655 Iterations, force evaluations = 119 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8853 | 1.8853 | 1.8853 | 0.0 | 97.65 Neigh | 0.019332 | 0.019332 | 0.019332 | 0.0 | 1.00 Comm | 0.015614 | 0.015614 | 0.015614 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01043 | | | 0.54 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8480.00 ave 8480 max 8480 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: 169584.0 ave 169584 max 169584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169584 Ave neighs/atom = 174.11088 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -4324.1442 0 -4324.1442 -1351.0571 10636.15 121 0 -4324.1495 0 -4324.1495 100.59594 10627.442 Loop time of 0.0438694 on 1 procs for 2 steps with 974 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 = -4324.14420466455 -4324.14873208052 -4324.14954694513 Force two-norm initial, final = 15.329716 0.21494284 Force max component initial, final = 13.088759 0.021919112 Final line search alpha, max atom move = 0.00034622589 7.5889641e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042468 | 0.042468 | 0.042468 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029918 | 0.00029918 | 0.00029918 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001102 | | | 2.51 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8465.00 ave 8465 max 8465 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: 169988.0 ave 169988 max 169988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169988 Ave neighs/atom = 174.52567 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.171 | 5.171 | 5.171 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4324.1495 0 -4324.1495 100.59594 Loop time of 1.491e-06 on 1 procs for 0 steps with 974 atoms 134.1% 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 | | 1.491e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8465.00 ave 8465 max 8465 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: 170004.0 ave 170004 max 170004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170004 Ave neighs/atom = 174.54209 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.171 | 5.171 | 5.171 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 -4324.1495 -4324.1495 27.486344 109.95331 3.5164419 100.59594 100.59594 0.14738806 299.70126 1.9391618 2.198106 146.21134 Loop time of 1.518e-06 on 1 procs for 0 steps with 974 atoms 197.6% 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 | | 1.518e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8465.00 ave 8465 max 8465 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85002.0 ave 85002 max 85002 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170004.0 ave 170004 max 170004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170004 Ave neighs/atom = 174.54209 Neighbor list builds = 0 Dangerous builds = 0 974 -4324.14954694513 eV 2.19810602563632 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02