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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -40.359652 0.0000000) to (6.1787846 40.359652 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1787846 5.0449565 5.8254140 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -40.359652 0.0000000) to (6.1787846 40.359652 8.7381210) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1787846 5.0449565 5.8254140 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -40.359652 0.0000000) to (6.1787846 40.359652 8.7381210) create_atoms CPU = 0.000 seconds 198 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 384 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1618.33 0 -1618.33 7329.1787 32 0 -1622.8931 0 -1622.8931 22961.25 Loop time of 0.764723 on 1 procs for 32 steps with 384 atoms 93.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1618.33004708189 -1622.89164983086 -1622.89307522311 Force two-norm initial, final = 7.9478992 0.12843927 Force max component initial, final = 1.3510106 0.014978041 Final line search alpha, max atom move = 1.0000000 0.014978041 Iterations, force evaluations = 32 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76179 | 0.76179 | 0.76179 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014935 | 0.0014935 | 0.0014935 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001442 | | | 0.19 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2574.00 ave 2574 max 2574 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: 21048.0 ave 21048 max 21048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21048 Ave neighs/atom = 54.812500 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1622.8931 0 -1622.8931 22961.25 4358.1134 39 0 -1623.1891 0 -1623.1891 476.59857 4384.6347 Loop time of 0.0970554 on 1 procs for 7 steps with 384 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 = -1622.89307522311 -1623.18805539163 -1623.18907917677 Force two-norm initial, final = 114.46164 3.1501695 Force max component initial, final = 89.103800 2.9175635 Final line search alpha, max atom move = 0.00016397506 0.00047840765 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.096028 | 0.096028 | 0.096028 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017974 | 0.00017974 | 0.00017974 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008477 | | | 0.87 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2574.00 ave 2574 max 2574 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: 21720.0 ave 21720 max 21720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21720 Ave neighs/atom = 56.562500 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1623.1891 0 -1623.1891 476.59857 Loop time of 1.655e-06 on 1 procs for 0 steps with 384 atoms 120.8% 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 | | 1.655e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2574.00 ave 2574 max 2574 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: 21408.0 ave 21408 max 21408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21408 Ave neighs/atom = 55.750000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.575 | 4.575 | 4.575 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 -1623.1891 -1623.1891 6.1906944 81.199355 8.7225099 476.59857 476.59857 406.23335 1072.4386 -48.876223 2.4992873 0.92519358 Loop time of 7.618e-06 on 1 procs for 0 steps with 384 atoms 131.3% 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 | | 7.618e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2574.00 ave 2574 max 2574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10704.0 ave 10704 max 10704 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21408.0 ave 21408 max 21408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21408 Ave neighs/atom = 55.750000 Neighbor list builds = 0 Dangerous builds = 0 384 -1623.18907917677 eV 2.49928725820088 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01