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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7242695 5.6655575 6.2546061 Created 620 atoms using lattice units in orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) create_atoms CPU = 0.002 seconds 620 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7242695 5.6655575 6.2546061 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) create_atoms CPU = 0.001 seconds 629 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 24 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1247 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_343168101490_001#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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.030 | 5.030 | 5.030 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4913.3502 0 -4913.3502 64333.806 523 0 -5286.188 0 -5286.188 10738.505 Loop time of 83.2998 on 1 procs for 523 steps with 1247 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 = -4913.3501959578 -5286.18307307221 -5286.18795937788 Force two-norm initial, final = 456.00049 0.26470181 Force max component initial, final = 123.60152 0.076852690 Final line search alpha, max atom move = 1.0000000 0.076852690 Iterations, force evaluations = 523 979 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 83.016 | 83.016 | 83.016 | 0.0 | 99.66 Neigh | 0.14448 | 0.14448 | 0.14448 | 0.0 | 0.17 Comm | 0.064565 | 0.064565 | 0.064565 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0745 | | | 0.09 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4998.00 ave 4998 max 4998 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: 118574.0 ave 118574 max 118574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118574 Ave neighs/atom = 95.087410 Neighbor list builds = 16 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 523 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press Volume 523 0 -5286.188 0 -5286.188 10738.505 14691.719 548 0 -5293.6696 0 -5293.6696 -20.271034 14768.601 Loop time of 2.53437 on 1 procs for 25 steps with 1247 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 = -5286.18795937789 -5293.66827213201 -5293.66956610483 Force two-norm initial, final = 479.57573 5.3984565 Force max component initial, final = 293.28963 3.5538828 Final line search alpha, max atom move = 0.00090706126 0.0032235894 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5167 | 2.5167 | 2.5167 | 0.0 | 99.30 Neigh | 0.0087943 | 0.0087943 | 0.0087943 | 0.0 | 0.35 Comm | 0.0013195 | 0.0013195 | 0.0013195 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0076 | | | 0.30 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4987.00 ave 4987 max 4987 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: 118852.0 ave 118852 max 118852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118852 Ave neighs/atom = 95.310345 Neighbor list builds = 1 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.169 | 5.169 | 5.169 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5293.6696 0 -5293.6696 -20.271034 Loop time of 2.273e-06 on 1 procs for 0 steps with 1247 atoms 176.0% 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 | | 2.273e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 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: 119150.0 ave 119150 max 119150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119150 Ave neighs/atom = 95.549318 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.169 | 5.169 | 5.169 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 -5293.6696 -5293.6696 31.119534 74.719958 6.3514029 -20.271034 -20.271034 376.20152 -320.0764 -116.93821 2.2030518 2357.6494 Loop time of 2.236e-06 on 1 procs for 0 steps with 1247 atoms 268.3% 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 | | 2.236e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59575.0 ave 59575 max 59575 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119150.0 ave 119150 max 119150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119150 Ave neighs/atom = 95.549318 Neighbor list builds = 0 Dangerous builds = 0 1247 -5293.66956610483 eV 2.20305180779206 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:26