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 -49.160835 0.0000000) to (24.580418 49.160835 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4325343 4.4325343 3.1472000 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -49.160835 0.0000000) to (24.580418 49.160835 3.1472000) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4325343 4.4325343 3.1472000 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.160835 0.0000000) to (24.580418 49.160835 3.1472000) create_atoms CPU = 0.001 seconds 245 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 = 8 32 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 = 489 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 = 8 32 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3117.6321 0 -3117.6321 85060.233 45 0 -3321.5063 0 -3321.5063 7101.7235 Loop time of 0.501388 on 1 procs for 45 steps with 489 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3117.63211235531 -3321.50317645359 -3321.50629143697 Force two-norm initial, final = 369.24573 0.23277402 Force max component initial, final = 128.97030 0.035800002 Final line search alpha, max atom move = 1.0000000 0.035800002 Iterations, force evaluations = 45 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48607 | 0.48607 | 0.48607 | 0.0 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083879 | 0.0083879 | 0.0083879 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00693 | | | 1.38 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3671.00 ave 3671 max 3671 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: 28664.0 ave 28664 max 28664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28664 Ave neighs/atom = 58.617587 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 = 8 32 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -3321.5063 0 -3321.5063 7101.7235 7606.1142 50 0 -3321.6878 0 -3321.6878 -111.89695 7623.5841 Loop time of 0.0607121 on 1 procs for 5 steps with 489 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 = -3321.50629143697 -3321.68748861095 -3321.68784756988 Force two-norm initial, final = 87.481896 1.7416037 Force max component initial, final = 81.179772 1.6666485 Final line search alpha, max atom move = 0.00022753891 0.00037922738 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055362 | 0.055362 | 0.055362 | 0.0 | 91.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011325 | 0.0011325 | 0.0011325 | 0.0 | 1.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004217 | | | 6.95 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3680.00 ave 3680 max 3680 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: 28706.0 ave 28706 max 28706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28706 Ave neighs/atom = 58.703476 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 = 8 32 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3321.6878 0 -3321.6878 -111.89695 Loop time of 1.0394e-05 on 1 procs for 0 steps with 489 atoms 163.6% 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 | | 1.039e-05 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3683.00 ave 3683 max 3683 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: 28636.0 ave 28636 max 28636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28636 Ave neighs/atom = 58.560327 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 = 8 32 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) = 4.595 | 4.595 | 4.595 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 -3321.6878 -3321.6878 24.588799 98.723707 3.1405117 -111.89695 -111.89695 -350.38318 -36.109866 50.802197 2.5233116 206.69802 Loop time of 9.432e-06 on 1 procs for 0 steps with 489 atoms 212.0% 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 | | 9.432e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3683.00 ave 3683 max 3683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14318.0 ave 14318 max 14318 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28636.0 ave 28636 max 28636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28636 Ave neighs/atom = 58.560327 Neighbor list builds = 0 Dangerous builds = 0 489 -3321.68784756988 eV 2.52331155094505 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