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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.555053 0.0000000) to (53.339413 43.555053 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1147382 5.3693566 5.8858683 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.555053 0.0000000) to (53.339413 43.555053 8.8288024) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1147382 5.3693566 5.8858683 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.555053 0.0000000) to (53.339413 43.555053 8.8288024) create_atoms CPU = 0.002 seconds 1756 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 64 atoms, new total = 3448 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14488.161 0 -14488.161 -4264.2277 143 0 -14605.512 0 -14605.512 -22445.381 Loop time of 29.5706 on 1 procs for 143 steps with 3448 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14488.1605657695 -14605.4986386914 -14605.5117425133 Force two-norm initial, final = 45.281619 0.31962900 Force max component initial, final = 5.9865126 0.059237493 Final line search alpha, max atom move = 1.0000000 0.059237493 Iterations, force evaluations = 143 254 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.444 | 29.444 | 29.444 | 0.0 | 99.57 Neigh | 0.059688 | 0.059688 | 0.059688 | 0.0 | 0.20 Comm | 0.024224 | 0.024224 | 0.024224 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04243 | | | 0.14 Nlocal: 3448.00 ave 3448 max 3448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8058.00 ave 8058 max 8058 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: 267076.0 ave 267076 max 267076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267076 Ave neighs/atom = 77.458237 Neighbor list builds = 3 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 143 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -14605.512 0 -14605.512 -22445.381 41022.164 156 0 -14611.223 0 -14611.223 1119.2191 40407.553 Loop time of 1.56829 on 1 procs for 13 steps with 3448 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 = -14605.5117425133 -14611.2188985741 -14611.2229604634 Force two-norm initial, final = 948.65524 6.5399534 Force max component initial, final = 797.51740 5.5044487 Final line search alpha, max atom move = 6.7240233e-05 0.00037012042 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5603 | 1.5603 | 1.5603 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009378 | 0.0009378 | 0.0009378 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007072 | | | 0.45 Nlocal: 3448.00 ave 3448 max 3448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8074.00 ave 8074 max 8074 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: 267152.0 ave 267152 max 267152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267152 Ave neighs/atom = 77.480278 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.824 | 5.824 | 5.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14611.223 0 -14611.223 1119.2191 Loop time of 1.948e-06 on 1 procs for 0 steps with 3448 atoms 205.3% 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 | | 1.948e-06 | | |100.00 Nlocal: 3448.00 ave 3448 max 3448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8111.00 ave 8111 max 8111 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: 268312.0 ave 268312 max 268312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268312 Ave neighs/atom = 77.816705 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.824 | 5.824 | 5.824 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 -14611.223 -14611.223 52.686357 87.110105 8.8043205 1119.2191 1119.2191 -215.58154 3709.4565 -136.21758 2.2993799 3173.8522 Loop time of 1.863e-06 on 1 procs for 0 steps with 3448 atoms 214.7% 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 | | 1.863e-06 | | |100.00 Nlocal: 3448.00 ave 3448 max 3448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8111.00 ave 8111 max 8111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134156.0 ave 134156 max 134156 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 268312.0 ave 268312 max 268312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 268312 Ave neighs/atom = 77.816705 Neighbor list builds = 0 Dangerous builds = 0 3448 -14611.2229604634 eV 2.299379851673 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31