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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -42.138139 0.0000000) to (14.898082 42.138139 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1345044 6.1967852 5.1100000 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.138139 0.0000000) to (14.898082 42.138139 5.1100000) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1345044 6.1967852 5.1100000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.138139 0.0000000) to (14.898082 42.138139 5.1100000) create_atoms CPU = 0.003 seconds 274 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_087820130586_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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1821.9702 0 -1821.9702 47960.674 104 0 -1919.4422 0 -1919.4422 5906.3247 Loop time of 4.59952 on 1 procs for 104 steps with 544 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 = -1821.97017837475 -1919.44064026407 -1919.44218423795 Force two-norm initial, final = 200.26841 0.11914124 Force max component initial, final = 61.575507 0.034585479 Final line search alpha, max atom move = 1.0000000 0.034585479 Iterations, force evaluations = 104 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5573 | 4.5573 | 4.5573 | 0.0 | 99.08 Neigh | 0.0084007 | 0.0084007 | 0.0084007 | 0.0 | 0.18 Comm | 0.017078 | 0.017078 | 0.017078 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01671 | | | 0.36 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3362.00 ave 3362 max 3362 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: 42036.0 ave 42036 max 42036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42036 Ave neighs/atom = 77.272059 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -1919.4422 0 -1919.4422 5906.3247 6415.8856 108 0 -1919.5098 0 -1919.5098 229.10617 6441.5319 Loop time of 0.132324 on 1 procs for 4 steps with 544 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 = -1919.44218423795 -1919.50847926389 -1919.50978220358 Force two-norm initial, final = 43.785737 1.9303254 Force max component initial, final = 36.272695 1.7249571 Final line search alpha, max atom move = 0.00025505929 0.00043996634 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13021 | 0.13021 | 0.13021 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004439 | 0.0004439 | 0.0004439 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001672 | | | 1.26 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3362.00 ave 3362 max 3362 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: 42032.0 ave 42032 max 42032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42032 Ave neighs/atom = 77.264706 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1919.5098 0 -1919.5098 229.10617 Loop time of 6.325e-06 on 1 procs for 0 steps with 544 atoms 158.1% 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 | | 6.325e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3362.00 ave 3362 max 3362 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: 42020.0 ave 42020 max 42020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42020 Ave neighs/atom = 77.242647 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.633 | 4.633 | 4.633 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 -1919.5098 -1919.5098 14.905547 84.545301 5.11154 229.10617 229.10617 206.70362 430.41126 50.203646 2.4080955 280.62474 Loop time of 6.766e-06 on 1 procs for 0 steps with 544 atoms 251.3% 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 | | 6.766e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3362.00 ave 3362 max 3362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21010.0 ave 21010 max 21010 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42020.0 ave 42020 max 42020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42020 Ave neighs/atom = 77.242647 Neighbor list builds = 0 Dangerous builds = 0 544 -1919.50978220358 eV 2.40809553307924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05