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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -70.148139 0.0000000) to (28.637858 70.148139 9.9204450) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8730859 6.0795054 6.6136300 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -70.148139 0.0000000) to (28.637858 70.148139 9.9204450) create_atoms CPU = 0.006 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8730859 6.0795054 6.6136300 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -70.148139 0.0000000) to (28.637858 70.148139 9.9204450) create_atoms CPU = 0.005 seconds 1203 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 34 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2398 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_651801486679_005#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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.051 | 6.051 | 6.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7963.951 0 -7963.951 3524.9238 88 0 -8041.5239 0 -8041.5239 1426.1585 Loop time of 5.23379 on 1 procs for 88 steps with 2398 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 = -7963.95103562588 -8041.51647886457 -8041.52387364403 Force two-norm initial, final = 31.817409 0.22007486 Force max component initial, final = 3.7919992 0.044300195 Final line search alpha, max atom move = 1.0000000 0.044300195 Iterations, force evaluations = 88 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.001 | 5.001 | 5.001 | 0.0 | 95.55 Neigh | 0.16176 | 0.16176 | 0.16176 | 0.0 | 3.09 Comm | 0.032075 | 0.032075 | 0.032075 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03891 | | | 0.74 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8938.00 ave 8938 max 8938 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: 335040.0 ave 335040 max 335040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335040 Ave neighs/atom = 139.71643 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.051 | 6.051 | 6.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -8041.5239 0 -8041.5239 1426.1585 39858.214 93 0 -8041.7185 0 -8041.7185 -52.5116 39932.241 Loop time of 0.24196 on 1 procs for 5 steps with 2398 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8041.52387364397 -8041.71700435567 -8041.71852584604 Force two-norm initial, final = 93.457815 2.3007713 Force max component initial, final = 92.818472 1.4998481 Final line search alpha, max atom move = 0.00016655670 0.00024980975 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23495 | 0.23495 | 0.23495 | 0.0 | 97.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014374 | 0.0014374 | 0.0014374 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005573 | | | 2.30 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8881.00 ave 8881 max 8881 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: 335024.0 ave 335024 max 335024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335024 Ave neighs/atom = 139.70976 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.189 | 6.189 | 6.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8041.7185 0 -8041.7185 -52.5116 Loop time of 6.254e-06 on 1 procs for 0 steps with 2398 atoms 191.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8886.00 ave 8886 max 8886 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: 334886.0 ave 334886 max 334886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334886 Ave neighs/atom = 139.65221 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.189 | 6.189 | 6.189 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 -8041.7185 -8041.7185 28.61035 140.91147 9.904993 -52.5116 -52.5116 -52.698938 -44.75212 -60.083742 2.6210636 842.52952 Loop time of 6.545e-06 on 1 procs for 0 steps with 2398 atoms 259.7% 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 | | 6.545e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8886.00 ave 8886 max 8886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167443.0 ave 167443 max 167443 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334886.0 ave 334886 max 334886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334886 Ave neighs/atom = 139.65221 Neighbor list builds = 0 Dangerous builds = 0 2398 -8041.71852609596 eV 2.62106358739187 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06