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 -60.968188 0.0000000) to (24.890159 60.968188 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9736381 5.2839096 5.7481359 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -60.968188 0.0000000) to (24.890159 60.968188 8.6222039) create_atoms CPU = 0.002 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9736381 5.2839096 5.7481359 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -60.968188 0.0000000) to (24.890159 60.968188 8.6222039) create_atoms CPU = 0.002 seconds 1205 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 8 36 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2400 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 8 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.997 | 5.997 | 5.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10472.998 0 -10472.998 9894.2693 39 0 -10656.173 0 -10656.173 7999.0808 Loop time of 0.90611 on 1 procs for 39 steps with 2400 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10472.9983140188 -10656.1633984135 -10656.1728501074 Force two-norm initial, final = 62.842218 0.32622250 Force max component initial, final = 7.6307201 0.036310606 Final line search alpha, max atom move = 1.0000000 0.036310606 Iterations, force evaluations = 39 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86978 | 0.86978 | 0.86978 | 0.0 | 95.99 Neigh | 0.021888 | 0.021888 | 0.021888 | 0.0 | 2.42 Comm | 0.0055545 | 0.0055545 | 0.0055545 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008888 | | | 0.98 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8231.00 ave 8231 max 8231 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: 318616.0 ave 318616 max 318616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318616 Ave neighs/atom = 132.75667 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 8 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.998 | 5.998 | 5.998 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -10656.173 0 -10656.173 7999.0808 26168.525 46 0 -10656.88 0 -10656.88 -5.9844409 26287.476 Loop time of 0.137643 on 1 procs for 7 steps with 2400 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 = -10656.1728501074 -10656.8796583809 -10656.8797480991 Force two-norm initial, final = 278.59385 0.66431453 Force max component initial, final = 262.84627 0.35213251 Final line search alpha, max atom move = 0.00038519189 0.00013563859 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13254 | 0.13254 | 0.13254 | 0.0 | 96.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074146 | 0.00074146 | 0.00074146 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004358 | | | 3.17 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8273.00 ave 8273 max 8273 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: 318430.0 ave 318430 max 318430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318430 Ave neighs/atom = 132.67917 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 8 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.136 | 6.136 | 6.136 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10656.88 0 -10656.88 -5.9844409 Loop time of 2.561e-06 on 1 procs for 0 steps with 2400 atoms 195.2% 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 | | 2.561e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8273.00 ave 8273 max 8273 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: 318194.0 ave 318194 max 318194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318194 Ave neighs/atom = 132.58083 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 8 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.136 | 6.136 | 6.136 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 -10656.88 -10656.88 24.888637 122.62888 8.6130108 -5.9844409 -5.9844409 16.506607 -13.02094 -21.438989 2.3412849 674.96939 Loop time of 2.36e-06 on 1 procs for 0 steps with 2400 atoms 211.9% 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 | | 2.36e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8273.00 ave 8273 max 8273 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159097.0 ave 159097 max 159097 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 318194.0 ave 318194 max 318194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318194 Ave neighs/atom = 132.58083 Neighbor list builds = 0 Dangerous builds = 0 2400 -10656.8797480991 eV 2.34128486460468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01