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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -51.521884 0.0000000) to (36.431474 51.521884 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4375334 4.9983917 4.4508129 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -51.521884 0.0000000) to (36.431474 51.521884 4.4508129) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4375334 4.9983917 4.4508129 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -51.521884 0.0000000) to (36.431474 51.521884 4.4508129) create_atoms CPU = 0.001 seconds 538 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 34 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1074 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6952.7878 0 -6952.7878 83974.101 75 0 -7293.4313 0 -7293.4313 10369.959 Loop time of 0.673661 on 1 procs for 75 steps with 1074 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 = -6952.78776953007 -7293.42488000788 -7293.43133653483 Force two-norm initial, final = 411.45845 0.35343628 Force max component initial, final = 111.08254 0.057037927 Final line search alpha, max atom move = 1.0000000 0.057037927 Iterations, force evaluations = 75 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66114 | 0.66114 | 0.66114 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005803 | 0.005803 | 0.005803 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006721 | | | 1.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4589.00 ave 4589 max 4589 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: 62944.0 ave 62944 max 62944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62944 Ave neighs/atom = 58.607076 Neighbor list builds = 0 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -7293.4313 0 -7293.4313 10369.959 16708.513 83 0 -7294.3568 0 -7294.3568 56.277305 16762.619 Loop time of 0.0507151 on 1 procs for 8 steps with 1074 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 = -7293.43133653483 -7294.35675529781 -7294.35679061662 Force two-norm initial, final = 288.65780 1.4022458 Force max component initial, final = 287.41876 1.0326998 Final line search alpha, max atom move = 0.00062473630 0.00064516508 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048349 | 0.048349 | 0.048349 | 0.0 | 95.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037661 | 0.00037661 | 0.00037661 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001989 | | | 3.92 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4585.00 ave 4585 max 4585 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: 63172.0 ave 63172 max 63172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63172 Ave neighs/atom = 58.819367 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.729 | 4.729 | 4.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7294.3568 0 -7294.3568 56.277305 Loop time of 1.523e-06 on 1 procs for 0 steps with 1074 atoms 131.3% 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 | | 1.523e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4585.00 ave 4585 max 4585 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: 63032.0 ave 63032 max 63032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63032 Ave neighs/atom = 58.689013 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.729 | 4.729 | 4.729 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 -7294.3568 -7294.3568 36.363955 103.73818 4.443571 56.277305 56.277305 21.313613 48.97312 98.545181 2.3787182 581.15751 Loop time of 1.579e-06 on 1 procs for 0 steps with 1074 atoms 190.0% 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 | | 1.579e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4585.00 ave 4585 max 4585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31516.0 ave 31516 max 31516 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63032.0 ave 63032 max 63032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63032 Ave neighs/atom = 58.689013 Neighbor list builds = 0 Dangerous builds = 0 1074 -7294.35679061662 eV 2.37871820221522 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42