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 -35.186765 0.0000000) to (7.0373531 35.186765 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2224118 4.2224118 3.1472000 Created 50 atoms using lattice units in orthogonal box = (0.0000000 -35.186765 0.0000000) to (7.0373531 35.186765 3.1472000) create_atoms CPU = 0.001 seconds 50 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2224118 4.2224118 3.1472000 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -35.186765 0.0000000) to (7.0373531 35.186765 3.1472000) create_atoms CPU = 0.000 seconds 51 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 = 3 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 100 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 = 3 23 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) = 4.362 | 4.362 | 4.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -667.48979 0 -667.48979 48675.486 37 0 -676.74799 0 -676.74799 10184.228 Loop time of 0.0942871 on 1 procs for 37 steps with 100 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 = -667.489790387805 -676.747433249386 -676.747994338593 Force two-norm initial, final = 36.041593 0.14494124 Force max component initial, final = 15.844538 0.061859713 Final line search alpha, max atom move = 1.0000000 0.061859713 Iterations, force evaluations = 37 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09081 | 0.09081 | 0.09081 | 0.0 | 96.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022058 | 0.0022058 | 0.0022058 | 0.0 | 2.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001271 | | | 1.35 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1535.00 ave 1535 max 1535 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: 5852.00 ave 5852 max 5852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5852 Ave neighs/atom = 58.520000 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 = 3 23 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -676.74799 0 -676.74799 10184.228 1558.63 46 0 -676.85061 0 -676.85061 432.88788 1563.7616 Loop time of 0.0171381 on 1 procs for 9 steps with 100 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -676.747994338593 -676.850565285625 -676.850613705396 Force two-norm initial, final = 28.038488 0.81035417 Force max component initial, final = 28.004438 0.51697026 Final line search alpha, max atom move = 0.0075814770 0.0039193982 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015602 | 0.015602 | 0.015602 | 0.0 | 91.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036685 | 0.00036685 | 0.00036685 | 0.0 | 2.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00117 | | | 6.82 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1535.00 ave 1535 max 1535 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: 5860.00 ave 5860 max 5860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5860 Ave neighs/atom = 58.600000 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 = 3 23 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) = 4.500 | 4.500 | 4.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -676.85061 0 -676.85061 432.88788 Loop time of 5.813e-06 on 1 procs for 0 steps with 100 atoms 120.4% 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 | | 5.813e-06 | | |100.00 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1535.00 ave 1535 max 1535 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: 5830.00 ave 5830 max 5830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5830 Ave neighs/atom = 58.300000 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 = 3 23 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) = 4.500 | 4.500 | 4.500 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 -676.85061 -676.85061 7.019351 70.904545 3.1419518 432.88788 432.88788 528.31505 358.0601 412.28851 2.5537247 82.947274 Loop time of 6.014e-06 on 1 procs for 0 steps with 100 atoms 149.7% 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 | | 6.014e-06 | | |100.00 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1535.00 ave 1535 max 1535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2915.00 ave 2915 max 2915 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5830.00 ave 5830 max 5830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5830 Ave neighs/atom = 58.300000 Neighbor list builds = 0 Dangerous builds = 0 100 -676.850613705396 eV 2.55372468284901 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