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 -33.896381 0.0000000) to (16.948191 33.896381 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0909425 4.0909425 3.1472000 Created 116 atoms using lattice units in orthogonal box = (0.0000000 -33.896381 0.0000000) to (16.948191 33.896381 3.1472000) create_atoms CPU = 0.002 seconds 116 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0909425 4.0909425 3.1472000 Created 117 atoms using lattice units in orthogonal box = (0.0000000 -33.896381 0.0000000) to (16.948191 33.896381 3.1472000) create_atoms CPU = 0.001 seconds 117 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 = 6 22 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 = 233 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 = 6 22 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) = 4.390 | 4.390 | 4.390 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1468.1994 0 -1468.1994 121378.41 35 0 -1574.8814 0 -1574.8814 28437.63 Loop time of 0.195571 on 1 procs for 35 steps with 233 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1468.19939929755 -1574.87996885757 -1574.88139416055 Force two-norm initial, final = 244.53182 0.18975268 Force max component initial, final = 111.81274 0.042622881 Final line search alpha, max atom move = 1.0000000 0.042622881 Iterations, force evaluations = 35 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18938 | 0.18938 | 0.18938 | 0.0 | 96.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003535 | 0.003535 | 0.003535 | 0.0 | 1.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002658 | | | 1.36 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2147.00 ave 2147 max 2147 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: 13718.0 ave 13718 max 13718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13718 Ave neighs/atom = 58.875536 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 = 6 22 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.390 | 4.390 | 4.390 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1574.8814 0 -1574.8814 28437.63 3616.0215 48 0 -1575.5581 0 -1575.5581 518.44025 3648.7213 Loop time of 0.0597679 on 1 procs for 13 steps with 233 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 = -1574.88139416055 -1575.55791319442 -1575.55812681923 Force two-norm initial, final = 134.60898 2.3408835 Force max component initial, final = 124.93664 1.7330948 Final line search alpha, max atom move = 0.0021336088 0.0036977463 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055038 | 0.055038 | 0.055038 | 0.0 | 92.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094537 | 0.00094537 | 0.00094537 | 0.0 | 1.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003784 | | | 6.33 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2152.00 ave 2152 max 2152 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: 13814.0 ave 13814 max 13814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13814 Ave neighs/atom = 59.287554 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 = 6 22 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1575.5581 0 -1575.5581 518.44025 Loop time of 6.575e-06 on 1 procs for 0 steps with 233 atoms 136.9% 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 | | 6.575e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2152.00 ave 2152 max 2152 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: 13642.0 ave 13642 max 13642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13642 Ave neighs/atom = 58.549356 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 = 6 22 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) = 4.528 | 4.528 | 4.528 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 -1575.5581 -1575.5581 16.94319 68.584372 3.1399328 518.44025 518.44025 760.78832 419.20903 375.3234 2.4613105 225.73248 Loop time of 8.721e-06 on 1 procs for 0 steps with 233 atoms 149.1% 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 | | 8.721e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2152.00 ave 2152 max 2152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6821.00 ave 6821 max 6821 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13642.0 ave 13642 max 13642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13642 Ave neighs/atom = 58.549356 Neighbor list builds = 0 Dangerous builds = 0 233 -1575.55812681923 eV 2.46131045980795 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