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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -48.392000 0.0000000) to (13.170634 48.392000 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6445575 5.3768889 5.7481360 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -48.392000 0.0000000) to (13.170634 48.392000 8.6222040) create_atoms CPU = 0.001 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6445575 5.3768889 5.7481360 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -48.392000 0.0000000) to (13.170634 48.392000 8.6222040) create_atoms CPU = 0.001 seconds 508 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 23 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1008 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_010613863288_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.499 | 5.499 | 5.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4436.4415 0 -4436.4415 7729.3542 36 0 -4468.3333 0 -4468.3333 7926.9692 Loop time of 0.782798 on 1 procs for 36 steps with 1008 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4436.44153158575 -4468.32941773768 -4468.33330178044 Force two-norm initial, final = 29.148823 0.19760794 Force max component initial, final = 5.0450912 0.012590563 Final line search alpha, max atom move = 1.0000000 0.012590563 Iterations, force evaluations = 36 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77328 | 0.77328 | 0.77328 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0048199 | 0.0048199 | 0.0048199 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004694 | | | 0.60 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6911.00 ave 6911 max 6911 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: 226720.0 ave 226720 max 226720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226720 Ave neighs/atom = 224.92063 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.499 | 5.499 | 5.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -4468.3333 0 -4468.3333 7926.9692 10990.781 41 0 -4468.5313 0 -4468.5313 -140.40864 11040.73 Loop time of 0.085164 on 1 procs for 5 steps with 1008 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 = -4468.33330178043 -4468.53087477374 -4468.5312885242 Force two-norm initial, final = 103.96095 1.7903118 Force max component initial, final = 87.901471 1.2114072 Final line search alpha, max atom move = 0.00029877247 0.00036193511 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082665 | 0.082665 | 0.082665 | 0.0 | 97.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042481 | 0.00042481 | 0.00042481 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002075 | | | 2.44 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6975.00 ave 6975 max 6975 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: 226200.0 ave 226200 max 226200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226200 Ave neighs/atom = 224.40476 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.637 | 5.637 | 5.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4468.5313 0 -4468.5313 -140.40864 Loop time of 2.068e-06 on 1 procs for 0 steps with 1008 atoms 193.4% 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 | | 2.068e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6944.00 ave 6944 max 6944 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: 225936.0 ave 225936 max 225936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225936 Ave neighs/atom = 224.14286 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.637 | 5.637 | 5.637 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 -4468.5313 -4468.5313 13.182587 97.193238 8.6170988 -140.40864 -140.40864 -171.91198 -73.624561 -175.68938 2.234984 383.0637 Loop time of 2.614e-06 on 1 procs for 0 steps with 1008 atoms 229.5% 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 | | 2.614e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6944.00 ave 6944 max 6944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112968.0 ave 112968 max 112968 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225936.0 ave 225936 max 225936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225936 Ave neighs/atom = 224.14286 Neighbor list builds = 0 Dangerous builds = 0 1008 -4468.5312885242 eV 2.23498401729576 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01