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 = 3.4871442 3.4871442 3.4871442 Created orthogonal box = (0.0000000 -44.657235 0.0000000) to (31.577434 44.657235 4.9315666) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3912692 5.9906047 4.9315666 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -44.657235 0.0000000) to (31.577434 44.657235 4.9315666) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3912692 5.9906047 4.9315666 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -44.657235 0.0000000) to (31.577434 44.657235 4.9315666) create_atoms CPU = 0.001 seconds 660 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 9 24 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5614.8954 0 -5614.8954 33822.304 74 0 -5788.049 0 -5788.049 -3104.1573 Loop time of 3.39588 on 1 procs for 74 steps with 1304 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5614.89539348506 -5788.04340678559 -5788.04899776672 Force two-norm initial, final = 313.84245 0.30226731 Force max component initial, final = 76.573278 0.042003105 Final line search alpha, max atom move = 1.0000000 0.042003105 Iterations, force evaluations = 74 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3569 | 3.3569 | 3.3569 | 0.0 | 98.85 Neigh | 0.013035 | 0.013035 | 0.013035 | 0.0 | 0.38 Comm | 0.013758 | 0.013758 | 0.013758 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01218 | | | 0.36 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7721.00 ave 7721 max 7721 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: 227456.0 ave 227456 max 227456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227456 Ave neighs/atom = 174.42945 Neighbor list builds = 1 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.468 | 5.468 | 5.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5788.049 0 -5788.049 -3104.1573 13908.605 78 0 -5788.1667 0 -5788.1667 -10.615877 13883.575 Loop time of 0.137247 on 1 procs for 4 steps with 1304 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 = -5788.04899776672 -5788.16547141579 -5788.1667392593 Force two-norm initial, final = 73.500202 0.60228690 Force max component initial, final = 72.672821 0.33098289 Final line search alpha, max atom move = 0.00020819664 6.8909527e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1352 | 0.1352 | 0.1352 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003569 | 0.0003569 | 0.0003569 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001688 | | | 1.23 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7728.00 ave 7728 max 7728 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: 227416.0 ave 227416 max 227416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227416 Ave neighs/atom = 174.39877 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.606 | 5.606 | 5.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5788.1667 0 -5788.1667 -10.615877 Loop time of 2.064e-06 on 1 procs for 0 steps with 1304 atoms 193.8% 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 | | 2.064e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7744.00 ave 7744 max 7744 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: 227464.0 ave 227464 max 227464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227464 Ave neighs/atom = 174.43558 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.606 | 5.606 | 5.606 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 -5788.1667 -5788.1667 31.473504 89.387174 4.9349303 -10.615877 -10.615877 -23.208309 29.582437 -38.221761 2.2943349 593.38508 Loop time of 2.811e-06 on 1 procs for 0 steps with 1304 atoms 0.0% 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 | | 2.811e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7744.00 ave 7744 max 7744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113732.0 ave 113732 max 113732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227464.0 ave 227464 max 227464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227464 Ave neighs/atom = 174.43558 Neighbor list builds = 0 Dangerous builds = 0 1304 -5788.1667392593 eV 2.29433492477296 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03