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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -35.226425 0.0000000) to (3.5226425 35.226425 3.5226425) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5226425 3.5226425 3.5226425 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -35.226425 0.0000000) to (3.5226425 35.226425 3.5226425) create_atoms CPU = 0.001 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5226425 3.5226425 3.5226425 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -35.226425 0.0000000) to (3.5226425 35.226425 3.5226425) create_atoms CPU = 0.000 seconds 42 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 1 12 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 80 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_381861218831_004#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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 1 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -339.24774 0 -339.24774 -0.034382737 1 0 -339.24774 0 -339.24774 -0.034382736 Loop time of 0.0252915 on 1 procs for 1 steps with 80 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 = -339.247742548104 -339.247742548104 -339.247742548093 Force two-norm initial, final = 1.2327620e-07 3.8864934e-08 Force max component initial, final = 6.1330860e-08 1.8991516e-08 Final line search alpha, max atom move = 1.0000000 1.8991516e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.024497 | 0.024497 | 0.024497 | 0.0 | 96.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046452 | 0.00046452 | 0.00046452 | 0.0 | 1.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003297 | | | 1.30 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6704.00 ave 6704 max 6704 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: 50080.0 ave 50080 max 50080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50080 Ave neighs/atom = 626.00000 Neighbor list builds = 0 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 1 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -339.24774 0 -339.24774 -0.034382736 874.25013 2 0 -339.24774 0 -339.24774 -3.539709e-06 874.25011 Loop time of 0.0250537 on 1 procs for 1 steps with 80 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 = -339.247742548093 -339.247742548093 -339.247742548109 Force two-norm initial, final = 3.2495776e-05 4.7377312e-08 Force max component initial, final = 1.8786821e-05 2.4164661e-08 Final line search alpha, max atom move = 1.0000000 2.4164661e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023736 | 0.023736 | 0.023736 | 0.0 | 94.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046143 | 0.00046143 | 0.00046143 | 0.0 | 1.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008562 | | | 3.42 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6704.00 ave 6704 max 6704 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: 50080.0 ave 50080 max 50080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50080 Ave neighs/atom = 626.00000 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 1 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 4.660 | 4.660 | 4.660 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -339.24774 0 -339.24774 -3.539709e-06 Loop time of 6.535e-06 on 1 procs for 0 steps with 80 atoms 183.6% 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 | | 6.535e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6704.00 ave 6704 max 6704 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: 50080.0 ave 50080 max 50080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50080 Ave neighs/atom = 626.00000 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 1 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 4.660 | 4.660 | 4.660 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 -339.24774 -339.24774 3.5226425 70.452849 3.5226425 -3.539709e-06 -3.539709e-06 1.6832805e-05 -4.4284869e-05 1.6832937e-05 2.4908844 1.0290943e-16 Loop time of 6.785e-06 on 1 procs for 0 steps with 80 atoms 162.1% 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 | | 6.785e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6704.00 ave 6704 max 6704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25040.0 ave 25040 max 25040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50080.0 ave 50080 max 50080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50080 Ave neighs/atom = 626.00000 Neighbor list builds = 0 Dangerous builds = 0 80 -339.247742548109 eV 2.49088437926783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00