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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -41.372574 0.0000000) to (8.2745149 41.372574 3.7004755) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9647089 4.9647089 3.7004755 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -41.372574 0.0000000) to (8.2745149 41.372574 3.7004755) create_atoms CPU = 0.000 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9647089 4.9647089 3.7004755 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -41.372574 0.0000000) to (8.2745149 41.372574 3.7004755) create_atoms CPU = 0.000 seconds 102 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 3 22 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 202 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 3 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -654.28593 0 -654.28593 179739.54 133 0 -806.22079 0 -806.22079 -1570.263 Loop time of 0.569121 on 1 procs for 133 steps with 202 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -654.28592800051 -806.220023008461 -806.220791455563 Force two-norm initial, final = 277.37923 0.082244604 Force max component initial, final = 104.55947 0.010729641 Final line search alpha, max atom move = 1.0000000 0.010729641 Iterations, force evaluations = 133 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55045 | 0.55045 | 0.55045 | 0.0 | 96.72 Neigh | 0.0057345 | 0.0057345 | 0.0057345 | 0.0 | 1.01 Comm | 0.0079181 | 0.0079181 | 0.0079181 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005015 | | | 0.88 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3253.00 ave 3253 max 3253 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: 30348.0 ave 30348 max 30348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30348 Ave neighs/atom = 150.23762 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 3 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.434 | 4.434 | 4.434 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -806.22079 0 -806.22079 -1570.263 2533.6267 342 0 -810.80095 0 -810.80095 613.16999 2472.8632 Loop time of 0.547057 on 1 procs for 209 steps with 202 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 = -806.220791455563 -810.800161168254 -810.800950620017 Force two-norm initial, final = 89.027451 2.0227168 Force max component initial, final = 63.670486 1.0355966 Final line search alpha, max atom move = 0.00087416702 0.00090528435 Iterations, force evaluations = 209 236 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49898 | 0.49898 | 0.49898 | 0.0 | 91.21 Neigh | 0.012008 | 0.012008 | 0.012008 | 0.0 | 2.19 Comm | 0.0068624 | 0.0068624 | 0.0068624 | 0.0 | 1.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02921 | | | 5.34 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3273.00 ave 3273 max 3273 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: 31776.0 ave 31776 max 31776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31776 Ave neighs/atom = 157.30693 Neighbor list builds = 6 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 3 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -810.80095 0 -810.80095 613.16999 Loop time of 2.096e-06 on 1 procs for 0 steps with 202 atoms 143.1% 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 | | 2.096e-06 | | |100.00 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3273.00 ave 3273 max 3273 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: 31868.0 ave 31868 max 31868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31868 Ave neighs/atom = 157.76238 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 3 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.571 | 4.571 | 4.571 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 -810.80095 -810.80095 8.4321955 75.857223 3.8660057 613.16999 613.16999 663.33368 615.1135 561.06279 2.2513446 137.53474 Loop time of 2.226e-06 on 1 procs for 0 steps with 202 atoms 224.6% 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 | | 2.226e-06 | | |100.00 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3273.00 ave 3273 max 3273 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15934.0 ave 15934 max 15934 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31868.0 ave 31868 max 31868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31868 Ave neighs/atom = 157.76238 Neighbor list builds = 0 Dangerous builds = 0 202 -810.800950620017 eV 2.25134464977915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01