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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -57.216438 0.0000000) to (35.035545 57.216438 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6508943 5.5367231 5.9326915 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.216438 0.0000000) to (35.035545 57.216438 8.8990373) create_atoms CPU = 0.006 seconds 1491 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6508943 5.5367231 5.9326915 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.216438 0.0000000) to (35.035545 57.216438 8.8990373) create_atoms CPU = 0.006 seconds 1491 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2952 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.960 | 6.960 | 6.960 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12501.372 0 -12501.372 6162.997 71 0 -12586.616 0 -12586.616 -9060.6423 Loop time of 5.56244 on 1 procs for 71 steps with 2952 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 = -12501.3718420573 -12586.6058739314 -12586.6156884495 Force two-norm initial, final = 83.568669 0.39242415 Force max component initial, final = 14.726890 0.051001753 Final line search alpha, max atom move = 1.0000000 0.051001753 Iterations, force evaluations = 71 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4286 | 5.4286 | 5.4286 | 0.0 | 97.59 Neigh | 0.066549 | 0.066549 | 0.066549 | 0.0 | 1.20 Comm | 0.029907 | 0.029907 | 0.029907 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03739 | | | 0.67 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10278.0 ave 10278 max 10278 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: 488326.0 ave 488326 max 488326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488326 Ave neighs/atom = 165.42209 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.579 | 6.579 | 6.579 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -12586.616 0 -12586.616 -9060.6423 35678.182 74 0 -12586.812 0 -12586.812 -4722.9143 35574.345 Loop time of 0.20989 on 1 procs for 3 steps with 2952 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12586.6156884495 -12586.8107585333 -12586.812421563 Force two-norm initial, final = 172.78002 0.48309050 Force max component initial, final = 153.47993 0.17177813 Final line search alpha, max atom move = 0.00010626089 1.8253298e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20438 | 0.20438 | 0.20438 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010727 | 0.0010727 | 0.0010727 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004438 | | | 2.11 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10314.0 ave 10314 max 10314 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: 452894.0 ave 452894 max 452894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452894 Ave neighs/atom = 153.41938 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.717 | 6.717 | 6.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12586.812 0 -12586.812 -4722.9143 Loop time of 6.395e-06 on 1 procs for 0 steps with 2952 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10320.0 ave 10320 max 10320 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: 465676.0 ave 465676 max 465676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 465676 Ave neighs/atom = 157.74932 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.717 | 6.717 | 6.717 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 -12586.812 -12586.812 35.010102 114.43288 8.8795859 -4722.9143 -4722.9143 7.573166 -14184.036 7.7195326 2.3470408 901.24498 Loop time of 7.247e-06 on 1 procs for 0 steps with 2952 atoms 276.0% 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 | | 7.247e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10320.0 ave 10320 max 10320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 232838.0 ave 232838 max 232838 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 465676.0 ave 465676 max 465676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 465676 Ave neighs/atom = 157.74932 Neighbor list builds = 0 Dangerous builds = 0 2952 -12586.812421563 eV 2.34704078524349 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06