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 = 3.7004859 3.7004859 3.7004859 Created orthogonal box = (0.0000000 -65.363614 0.0000000) to (37.737700 65.363614 6.4094297) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8058000 5.8659654 6.4094297 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -65.363614 0.0000000) to (37.737700 65.363614 6.4094297) create_atoms CPU = 0.009 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8058000 5.8659654 6.4094297 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -65.363614 0.0000000) to (37.737700 65.363614 6.4094297) create_atoms CPU = 0.008 seconds 1250 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 14 49 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 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2494 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_857282754307_003#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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 5.190 | 5.190 | 5.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3369.6141 0 -3369.6141 34995.399 93 0 -3731.1027 0 -3731.1027 -1160.1405 Loop time of 1.56863 on 1 procs for 93 steps with 2494 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 = -3369.61411915608 -3731.09899624169 -3731.10269629536 Force two-norm initial, final = 807.66083 0.23621286 Force max component initial, final = 303.03651 0.086444327 Final line search alpha, max atom move = 1.0000000 0.086444327 Iterations, force evaluations = 93 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4489 | 1.4489 | 1.4489 | 0.0 | 92.37 Neigh | 0.048011 | 0.048011 | 0.048011 | 0.0 | 3.06 Comm | 0.028342 | 0.028342 | 0.028342 | 0.0 | 1.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04337 | | | 2.76 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6773.00 ave 6773 max 6773 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: 134380.0 ave 134380 max 134380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134380 Ave neighs/atom = 53.881315 Neighbor list builds = 2 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.191 | 5.191 | 5.191 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -3731.1027 0 -3731.1027 -1160.1405 31619.927 95 0 -3731.1147 0 -3731.1147 1.9674551 31586.783 Loop time of 0.0461738 on 1 procs for 2 steps with 2494 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 = -3731.10269629536 -3731.11470347157 -3731.11471498468 Force two-norm initial, final = 39.678093 0.26388253 Force max component initial, final = 23.897935 0.095583366 Final line search alpha, max atom move = 0.0015923992 0.00015220688 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042275 | 0.042275 | 0.042275 | 0.0 | 91.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00070259 | 0.00070259 | 0.00070259 | 0.0 | 1.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003196 | | | 6.92 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6801.00 ave 6801 max 6801 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: 134602.0 ave 134602 max 134602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134602 Ave neighs/atom = 53.970329 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 5.329 | 5.329 | 5.329 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3731.1147 0 -3731.1147 1.9674551 Loop time of 6.335e-06 on 1 procs for 0 steps with 2494 atoms 189.4% 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 | | 6.335e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6801.00 ave 6801 max 6801 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: 134606.0 ave 134606 max 134606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134606 Ave neighs/atom = 53.971933 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 5.329 | 5.329 | 5.329 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 -3731.1147 -3731.1147 37.723065 130.68356 6.4073356 1.9674551 1.9674551 4.8463953 2.9240738 -1.8681038 2.2921496 732.97214 Loop time of 7.317e-06 on 1 procs for 0 steps with 2494 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 | | 7.317e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6801.00 ave 6801 max 6801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67303.0 ave 67303 max 67303 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134606.0 ave 134606 max 134606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134606 Ave neighs/atom = 53.971933 Neighbor list builds = 0 Dangerous builds = 0 2494 -3731.11471498468 eV 2.29214960925846 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02