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 12.807256933928919 -51.23307774596469 51.23307774596469 0 4.05001024902 units box create_box 2 whole Created orthogonal box = (0 -51.2331 0) to (12.8073 51.2331 4.05001) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 51.23307774596469 INF INF units box lattice fcc 4.05001024902 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.1229 5.1229 4.05001 create_atoms 1 region upper Created 162 atoms group upper type 1 162 atoms in group upper mass 1 26.981538 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 region lower block INF INF -51.23307774596469 0.0 INF INF units box lattice fcc 4.05001024902 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.1229 5.1229 4.05001 create_atoms 2 region lower Created 162 atoms group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 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 = 4 28 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 6 atoms, new total = 318 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 = 4 28 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) = 4.386 | 4.386 | 4.386 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1061.0523 0 -1061.0523 11418.483 341 0 -1074.1872 0 -1074.1872 -36.395014 Loop time of 0.926027 on 1 procs for 341 steps with 318 atoms 50.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1061.0522733 -1074.18718617 -1074.18718617 Force two-norm initial, final = 27.9755 8.71492e-06 Force max component initial, final = 7.10031 1.3418e-06 Final line search alpha, max atom move = 1 1.3418e-06 Iterations, force evaluations = 341 673 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91298 | 0.91298 | 0.91298 | 0.0 | 98.59 Neigh | 0.00072813 | 0.00072813 | 0.00072813 | 0.0 | 0.08 Comm | 0.0079679 | 0.0079679 | 0.0079679 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004348 | | | 0.47 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3662 ave 3662 max 3662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34712 ave 34712 max 34712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34712 Ave neighs/atom = 109.157 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) = 4.386 | 4.386 | 4.386 Mbytes Step Temp E_pair E_mol TotEng Press Volume 341 0 -1074.1872 0 -1074.1872 -36.395014 5314.8705 1341 0 -1074.1914 0 -1074.1914 745.07764 5309.3276 Loop time of 2.55755 on 1 procs for 1000 steps with 318 atoms 57.1% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1074.18718617 -1074.19136524 -1074.19136525 Force two-norm initial, final = 4.6443 0.00736373 Force max component initial, final = 4.44361 0.00639725 Final line search alpha, max atom move = 1 0.00639725 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3353 | 2.3353 | 2.3353 | 0.0 | 91.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021709 | 0.021709 | 0.021709 | 0.0 | 0.85 Output | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2005 | | | 7.84 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3496 ave 3496 max 3496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31603 ave 31603 max 31603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31603 Ave neighs/atom = 99.3805 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 = 4 28 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) = 4.523 | 4.523 | 4.523 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1074.1914 0 -1074.1914 745.07764 Loop time of 0 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3499 ave 3499 max 3499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32033 ave 32033 max 32033 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 = 32033 Ave neighs/atom = 100.733 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) = 4.523 | 4.523 | 4.523 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -1074.1914 12.778742 102.46616 4.0548144 745.07764 1.9261754 2232.3348 0.97196082 -1074.1914 2.6020691 205.09123 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3499 ave 3499 max 3499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32033 ave 32033 max 32033 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36788 ave 36788 max 36788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36788 Ave neighs/atom = 115.686 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_036.8699/energy.out -1074.191365247 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_036.8699/mindistance.out 2.60206911610915 write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03