LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.05001024902 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 region whole block 0 75.33454535563214 -75.33859536588116 75.33859536588116 0 4.05001024902 units box create_box 2 whole Created orthogonal box = (0 -75.3386 0) to (75.3345 75.3386 4.05001) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 75.33859536588116 INF INF units box lattice fcc 4.05001024902 orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.66098 5.66098 4.05001 create_atoms 1 region upper Created 1386 atoms group upper type 1 1386 atoms in group upper mass 1 26.981538 displace_atoms upper move 8.370483856982224 0 0.3333333333333333 region lower block INF INF -75.33859536588116 0.0 INF INF units box lattice fcc 4.05001024902 orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.66098 5.66098 4.05001 create_atoms 2 region lower Created 1386 atoms group lower type 2 1386 atoms in group lower displace_atoms lower move -8.370483856982224 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Sturgeon_Laird_Al__MO_120808805541_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02500512451 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 20 40 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: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Deleted 34 atoms, new total = 2738 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 20 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Per MPI rank memory allocation (min/avg/max) = 9.925 | 9.925 | 9.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9234.9686 0 -9234.9686 218.88333 479 0 -9260.1807 0 -9260.1807 -5098.6312 Loop time of 11.8191 on 1 procs for 479 steps with 2738 atoms 46.1% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9234.96860168 -9260.18070959 -9260.18070959 Force two-norm initial, final = 27.6942 2.14538e-06 Force max component initial, final = 5.2398 3.8571e-07 Final line search alpha, max atom move = 1 3.8571e-07 Iterations, force evaluations = 479 950 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.616 | 11.616 | 11.616 | 0.0 | 98.28 Neigh | 0.018867 | 0.018867 | 0.018867 | 0.0 | 0.16 Comm | 0.10459 | 0.10459 | 0.10459 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08003 | | | 0.68 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15325 ave 15325 max 15325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 258151 ave 258151 max 258151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258151 Ave neighs/atom = 94.2845 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 9.925 | 9.925 | 9.925 Mbytes Step Temp E_pair E_mol TotEng Press Volume 479 0 -9260.1807 0 -9260.1807 -5098.6312 45972.467 1479 0 -9260.4804 0 -9260.4804 -1392.204 45746.943 Loop time of 25.3276 on 1 procs for 1000 steps with 2738 atoms 46.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -9260.18070959 -9260.48035932 -9260.48035944 Force two-norm initial, final = 163.037 0.053353 Force max component initial, final = 124.367 0.0484873 Final line search alpha, max atom move = 0.0640847 0.00310729 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.038 | 24.038 | 24.038 | 0.0 | 94.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.25418 | 0.25418 | 0.25418 | 0.0 | 1.00 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.035 | | | 4.09 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15327 ave 15327 max 15327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237923 ave 237923 max 237923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237923 Ave neighs/atom = 86.8966 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 compute csym all centro/atom fcc compute csymsum all reduce sum c_csym compute eng all pe/atom compute eatoms all reduce sum c_eng compute distance all pair/local dist compute mindist all reduce min c_distance reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 20 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 9.056 | 9.056 | 9.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9260.4804 0 -9260.4804 -1392.204 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2738 atoms 0.0% CPU use with 1 MPI tasks x no 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 | | 9.537e-07 | | |100.00 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15327 ave 15327 max 15327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 264663 ave 264663 max 264663 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264663 Ave neighs/atom = 96.6629 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms c_mindist c_csymsum run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 9.056 | 9.056 | 9.056 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -9260.4804 75.285298 150.67719 4.0327787 -1392.204 0.23684061 -4178.5399 1.6909245 -9260.4804 2.5201835 986.68961 Loop time of 0 on 1 procs for 0 steps with 2738 atoms 0.0% CPU use with 1 MPI tasks x no 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 | | 0 | | | 0.00 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15327 ave 15327 max 15327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 264663 ave 264663 max 264663 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 315148 ave 315148 max 315148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315148 Ave neighs/atom = 115.102 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_072.5077/energy.out -9260.48035943831 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.5077/numatoms.out 2738 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_072.5077/mindistance.out 2.52018347337387 write_dump all cfg output/dump_072.5077/dump_post.cfg mass type xs ys zs id type xs ys zs c_csym c_eng modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_072.5077/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:37