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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -36.580913 0.0000000) to (25.866612 36.580913 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7481360 4.7419702 4.9780318 Created 430 atoms using lattice units in orthogonal box = (0.0000000 -36.580913 0.0000000) to (25.866612 36.580913 4.9780318) create_atoms CPU = 0.003 seconds 430 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7481360 4.7419702 4.9780318 Created 438 atoms using lattice units in orthogonal box = (0.0000000 -36.580913 0.0000000) to (25.866612 36.580913 4.9780318) create_atoms CPU = 0.002 seconds 438 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 17 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 864 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.395 | 5.395 | 5.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3782.0866 0 -3782.0866 8454.2005 106 0 -3827.3699 0 -3827.3699 12546.87 Loop time of 5.89641 on 1 procs for 106 steps with 864 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 = -3782.08661256988 -3827.36674512905 -3827.3699150773 Force two-norm initial, final = 29.205735 0.18550720 Force max component initial, final = 4.7699851 0.029753887 Final line search alpha, max atom move = 1.0000000 0.029753887 Iterations, force evaluations = 106 199 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8082 | 5.8082 | 5.8082 | 0.0 | 98.50 Neigh | 0.029627 | 0.029627 | 0.029627 | 0.0 | 0.50 Comm | 0.03407 | 0.03407 | 0.03407 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02448 | | | 0.42 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7168.00 ave 7168 max 7168 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: 213324.0 ave 213324 max 213324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213324 Ave neighs/atom = 246.90278 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -3827.3699 0 -3827.3699 12546.87 9420.6691 117 0 -3828.0312 0 -3828.0312 -24.244603 9487.1247 Loop time of 0.382085 on 1 procs for 11 steps with 864 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3827.36991507729 -3828.03110819072 -3828.03117144446 Force two-norm initial, final = 153.51035 0.72377895 Force max component initial, final = 131.01588 0.49902717 Final line search alpha, max atom move = 0.0023725176 0.0011839507 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37358 | 0.37358 | 0.37358 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019302 | 0.0019302 | 0.0019302 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006572 | | | 1.72 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7146.00 ave 7146 max 7146 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: 212880.0 ave 212880 max 212880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212880 Ave neighs/atom = 246.38889 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.529 | 5.529 | 5.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3828.0312 0 -3828.0312 -24.244603 Loop time of 6.155e-06 on 1 procs for 0 steps with 864 atoms 178.7% 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 | | 6.155e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7146.00 ave 7146 max 7146 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: 212558.0 ave 212558 max 212558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212558 Ave neighs/atom = 246.01620 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.529 | 5.529 | 5.529 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 -3828.0312 -3828.0312 25.772122 73.901514 4.981167 -24.244603 -24.244603 -15.399849 -85.127275 27.793315 2.3339861 663.55751 Loop time of 6.856e-06 on 1 procs for 0 steps with 864 atoms 262.5% 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 | | 6.856e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7146.00 ave 7146 max 7146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106279.0 ave 106279 max 106279 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212558.0 ave 212558 max 212558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212558 Ave neighs/atom = 246.01620 Neighbor list builds = 0 Dangerous builds = 0 864 -3808.54827371132 eV 2.333986066066 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07