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 -38.555982 0.0000000) to (27.263196 38.555982 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2613186 6.0877866 5.1068645 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.555982 0.0000000) to (27.263196 38.555982 5.1068645) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2613186 6.0877866 5.1068645 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.555982 0.0000000) to (27.263196 38.555982 5.1068645) create_atoms CPU = 0.001 seconds 458 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 23 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3520.3626 0 -3520.3626 94619.951 704 0 -3899.2684 0 -3899.2684 6374.2137 Loop time of 104.129 on 1 procs for 704 steps with 914 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 = -3520.36263576035 -3899.26469939407 -3899.26837977068 Force two-norm initial, final = 343.84412 0.21575966 Force max component initial, final = 79.896288 0.045682499 Final line search alpha, max atom move = 1.0000000 0.045682499 Iterations, force evaluations = 704 1319 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 103.84 | 103.84 | 103.84 | 0.0 | 99.73 Neigh | 0.14764 | 0.14764 | 0.14764 | 0.0 | 0.14 Comm | 0.074074 | 0.074074 | 0.074074 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06462 | | | 0.06 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 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: 102638.0 ave 102638 max 102638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102638 Ave neighs/atom = 112.29540 Neighbor list builds = 21 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 704 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 704 0 -3899.2684 0 -3899.2684 6374.2137 10736.256 734 0 -3910.8364 0 -3910.8364 1.8227418 10751.167 Loop time of 3.09429 on 1 procs for 30 steps with 914 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 = -3899.26837977068 -3910.83613206422 -3910.83639768356 Force two-norm initial, final = 581.39378 1.0274110 Force max component initial, final = 430.61855 0.40282639 Final line search alpha, max atom move = 0.00051344995 0.00020683119 Iterations, force evaluations = 30 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0842 | 3.0842 | 3.0842 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001513 | 0.001513 | 0.001513 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008544 | | | 0.28 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021.00 ave 5021 max 5021 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: 102686.0 ave 102686 max 102686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102686 Ave neighs/atom = 112.34792 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3910.8364 0 -3910.8364 1.8227418 Loop time of 2.597e-06 on 1 procs for 0 steps with 914 atoms 154.0% 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 | | 2.597e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5106.00 ave 5106 max 5106 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: 102494.0 ave 102494 max 102494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102494 Ave neighs/atom = 112.13786 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.105 | 5.105 | 5.105 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 -3910.8364 -3910.8364 28.03385 77.230239 4.965757 1.8227418 1.8227418 25.256924 38.583197 -58.371897 2.2891883 1738.5127 Loop time of 2.551e-06 on 1 procs for 0 steps with 914 atoms 196.0% 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 | | 2.551e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5106.00 ave 5106 max 5106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51247.0 ave 51247 max 51247 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102494.0 ave 102494 max 102494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102494 Ave neighs/atom = 112.13786 Neighbor list builds = 0 Dangerous builds = 0 914 -3910.83639768356 eV 2.28918834191002 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:47