LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.031999975442886*${_u_distance} variable lattice_constant_converted equal 4.031999975442886*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 65.63620424371317*${_u_distance} variable xmax_converted equal 65.63620424371317*1 variable ymin_converted equal -65.6402362436886*${_u_distance} variable ymin_converted equal -65.6402362436886*1 variable ymax_converted equal 65.6402362436886*${_u_distance} variable ymax_converted equal 65.6402362436886*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031999975442886*${_u_distance} variable zmax_converted equal 4.031999975442886*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03199997544289 Lattice spacing in x,y,z = 4.032 4.032 4.032 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6362042437132 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6362042437132 -65.6402362436886 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6362042437132 -65.6402362436886 65.6402362436886 ${zmin_converted} ${zmax_converted} units box region whole block 0 65.6362042437132 -65.6402362436886 65.6402362436886 0 ${zmax_converted} units box region whole block 0 65.6362042437132 -65.6402362436886 65.6402362436886 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -65.6402 0) to (65.6362 65.6402 4.032) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 65.6402362436886 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69673 5.69673 4.032 create_atoms 1 region upper Created 1061 atoms create_atoms CPU = 0.000406981 secs group upper type 1 1061 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.325469268244868 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -65.6402362436886 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69673 5.69673 4.032 create_atoms 2 region lower Created 1061 atoms create_atoms CPU = 0.000329971 secs group lower type 2 1061 atoms in group lower displace_atoms lower move -7.325469268244868 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000 pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.03199997544289 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01599998772144 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 15 30 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: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2092 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 15 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.932 | 9.932 | 9.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6993.7216 0 -6993.7216 -1738.8054 291 0 -7021.67 0 -7021.67 -9272.1842 Loop time of 4.4857 on 1 procs for 291 steps with 2092 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6993.72155881 -7021.66998673 -7021.66998673 Force two-norm initial, final = 17.4793 3.99037e-05 Force max component initial, final = 3.52696 9.96962e-06 Final line search alpha, max atom move = 1 9.96962e-06 Iterations, force evaluations = 291 544 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3721 | 4.3721 | 4.3721 | 0.0 | 97.47 Neigh | 0.043994 | 0.043994 | 0.043994 | 0.0 | 0.98 Comm | 0.044151 | 0.044151 | 0.044151 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02542 | | | 0.57 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13713 ave 13713 max 13713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 367710 ave 367710 max 367710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367710 Ave neighs/atom = 175.77 Neighbor list builds = 6 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 (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 9.932 | 9.932 | 9.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 291 0 -7021.67 0 -7021.67 -9272.1842 34742.743 1291 0 -7022.3383 0 -7022.3383 -2991.3978 34466.486 Loop time of 17.4095 on 1 procs for 1000 steps with 2092 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -7021.66998673 -7022.33832617 -7022.33832618 Force two-norm initial, final = 210.742 0.000177602 Force max component initial, final = 169.945 0.000174257 Final line search alpha, max atom move = 1 0.000174257 Iterations, force evaluations = 1000 1993 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.796 | 16.796 | 16.796 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13392 | 0.13392 | 0.13392 | 0.0 | 0.77 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4795 | | | 2.75 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12983 ave 12983 max 12983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 367736 ave 367736 max 367736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367736 Ave neighs/atom = 175.782 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.0 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 15 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 9.434 | 9.434 | 9.434 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7022.3383 0 -7022.3383 -2991.3978 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2092 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12983 ave 12983 max 12983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 367960 ave 367960 max 367960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367960 Ave neighs/atom = 175.889 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 9.434 | 9.434 | 9.434 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 -7022.3383 -7022.3383 65.602904 131.28047 4.0019699 -2991.3978 -2991.3978 0.00083109625 -8974.2023 0.0080399923 2.6032986 177.73856 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2092 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12983 ave 12983 max 12983 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183980 ave 183980 max 183980 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 367960 ave 367960 max 367960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367960 Ave neighs/atom = 175.889 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.0209/numatoms.out 2092 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7022.33832617513-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7022.33832617513-2092*${isolated_atom_energy} variable adjusted_pe_metal equal -7022.33832617513-2092*0 print "${adjusted_pe_metal} eV" file output/dump_085.0209/energy.out -7022.33832617513 eV print "${mindist_metal} Angstroms" file output/dump_085.0209/mindistance.out 2.60329864791204 Angstroms write_dump all cfg output/dump_085.0209/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_085.0209/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:22