LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 3.32812592387 Lattice spacing in x,y,z = 3.32813 3.32813 3.32813 region whole block 0 50.03270339808386 -50.03603152400773 50.03603152400773 0 3.32812592387 units box create_box 2 whole Created orthogonal box = (0 -50.036 0) to (50.0327 50.036 3.32813) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 50.03603152400773 INF INF units box lattice fcc 3.32812592387 orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 3.54214 3.54214 3.32813 create_atoms 1 region upper Created 906 atoms group upper type 1 906 atoms in group upper mass 1 26.981538 displace_atoms upper move 6.764983370267808 0 0.3333333333333333 region lower block INF INF -50.03603152400773 0.0 INF INF units box lattice fcc 3.32812592387 orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 3.54214 3.54214 3.32813 create_atoms 2 region lower Created 906 atoms group lower type 2 906 atoms in group lower displace_atoms lower move -6.764983370267808 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial LennardJones612_UniversalShifted__MO_959249795837_002 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 1.66406296194 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 = 10.6239 ghost atom cutoff = 10.6239 binsize = 5.31195, bins = 10 19 1 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 28 atoms, new total = 1784 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 = 10.6239 ghost atom cutoff = 10.6239 binsize = 5.31195, bins = 10 19 1 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -39182.477 0 -39182.477 173596.98 525 0 -39749.32 0 -39749.32 -212291.51 Loop time of 18.0157 on 1 procs for 525 steps with 1784 atoms 50.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -39182.4774334 -39749.3195208 -39749.3195208 Force two-norm initial, final = 1478.39 0.000109725 Force max component initial, final = 449.54 2.65268e-05 Final line search alpha, max atom move = 1 2.65268e-05 Iterations, force evaluations = 525 1048 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.744 | 17.744 | 17.744 | 0.0 | 98.49 Neigh | 0.07804 | 0.07804 | 0.07804 | 0.0 | 0.43 Comm | 0.12281 | 0.12281 | 0.12281 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07033 | | | 0.39 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20591 ave 20591 max 20591 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 880520 ave 880520 max 880520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 880520 Ave neighs/atom = 493.565 Neighbor list builds = 2 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press Volume 525 0 -39749.32 0 -39749.32 -212291.51 16663.513 1525 0 -39752.835 0 -39752.835 -78498.488 16590.342 Loop time of 31.5327 on 1 procs for 1000 steps with 1784 atoms 58.2% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -39749.3195208 -39752.8350525 -39752.8350536 Force two-norm initial, final = 2213.85 0.430729 Force max component initial, final = 1662.71 0.22244 Final line search alpha, max atom move = 0.00162886 0.000362324 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.479 | 30.479 | 30.479 | 0.0 | 96.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.21935 | 0.21935 | 0.21935 | 0.0 | 0.70 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.8343 | | | 2.65 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20648 ave 20648 max 20648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 880845 ave 880845 max 880845 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 880845 Ave neighs/atom = 493.747 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 = 10.6239 ghost atom cutoff = 10.6239 binsize = 5.31195, bins = 10 19 1 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) = 11.3 | 11.3 | 11.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -39752.835 0 -39752.835 -78498.488 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20741 ave 20741 max 20741 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 881852 ave 881852 max 881852 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 = 881852 Ave neighs/atom = 494.312 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) = 11.3 | 11.3 | 11.3 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -39752.835 49.892425 100.07206 3.3228282 -78498.488 -21.42139 -235458.08 -15.965483 -39752.835 2.1787559 205.6086 Loop time of 0 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20741 ave 20741 max 20741 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 881852 ave 881852 max 881852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 979488 ave 979488 max 979488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 979488 Ave neighs/atom = 549.04 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_007.6281/energy.out -39752.8350536074 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_007.6281/numatoms.out 1784 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_007.6281/mindistance.out 2.17875594168504 write_dump all cfg output/dump_007.6281/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_007.6281/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:49