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 4.050180745124819*${_u_distance} variable lattice_constant_converted equal 4.050180745124819*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 47.40615020586081*${_u_distance} variable xmax_converted equal 47.40615020586081*1 variable ymin_converted equal -47.410200386605936*${_u_distance} variable ymin_converted equal -47.410200386605936*1 variable ymax_converted equal 47.410200386605936*${_u_distance} variable ymax_converted equal 47.410200386605936*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050180745124819*${_u_distance} variable zmax_converted equal 4.050180745124819*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05018074512482 Lattice spacing in x,y,z = 4.05018 4.05018 4.05018 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 47.4061502058608 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4061502058608 -47.4102003866059 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4061502058608 -47.4102003866059 47.4102003866059 ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4061502058608 -47.4102003866059 47.4102003866059 0 ${zmax_converted} units box region whole block 0 47.4061502058608 -47.4102003866059 47.4102003866059 0 4.05018074512482 units box create_box 2 whole Created orthogonal box = (0 -47.4102 0) to (47.4062 47.4102 4.05018) 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 47.4102003866059 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 lattice fcc 4.05018074512482 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.19045 5.19045 4.05018 create_atoms 1 region upper Created 550 atoms create_atoms CPU = 0.000200987 secs group upper type 1 550 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.267114959823831 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -47.4102003866059 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 lattice fcc 4.05018074512482 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.19045 5.19045 4.05018 create_atoms 2 region lower Created 550 atoms create_atoms CPU = 8.79765e-05 secs group lower type 2 550 atoms in group lower displace_atoms lower move -5.267114959823831 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005 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*4.05018074512482 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02509037256241 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 12 23 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 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1074 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 12 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3825.7813 0 -3825.7813 -4296.4048 152 0 -3836.187 0 -3836.187 -7118.5646 Loop time of 1.04352 on 1 procs for 152 steps with 1074 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3825.78125842 -3836.18704511 -3836.18704511 Force two-norm initial, final = 6.97147 0.0062857 Force max component initial, final = 1.90548 0.00155147 Final line search alpha, max atom move = 0.000244141 3.78776e-07 Iterations, force evaluations = 152 311 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0198 | 1.0198 | 1.0198 | 0.0 | 97.72 Neigh | 0.004153 | 0.004153 | 0.004153 | 0.0 | 0.40 Comm | 0.012468 | 0.012468 | 0.012468 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007124 | | | 0.68 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7443 ave 7443 max 7443 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: 149328 ave 149328 max 149328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149328 Ave neighs/atom = 139.039 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 (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press Volume 152 0 -3836.187 0 -3836.187 -7118.5646 18205.847 170 0 -3836.4957 0 -3836.4957 -1151.9074 18062.101 Loop time of 0.242162 on 1 procs for 18 steps with 1074 atoms 103.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3836.18704511 -3836.49568045 -3836.49568045 Force two-norm initial, final = 107.333 0.11074 Force max component initial, final = 78.5026 0.0683496 Final line search alpha, max atom move = 8.92985e-07 6.10352e-08 Iterations, force evaluations = 18 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23107 | 0.23107 | 0.23107 | 0.0 | 95.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026066 | 0.0026066 | 0.0026066 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008483 | | | 3.50 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7792 ave 7792 max 7792 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: 149504 ave 149504 max 149504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149504 Ave neighs/atom = 139.203 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 -9.5367431640625e-07 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 12 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.40393 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) = 5.17 | 5.17 | 5.17 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3836.4957 0 -3836.4957 -1151.9074 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1074 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 | | 2.146e-06 | | |100.00 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7839 ave 7839 max 7839 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: 149608 ave 149608 max 149608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149608 Ave neighs/atom = 139.3 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) = 5.17 | 5.17 | 5.17 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 -3836.4957 -3836.4957 47.249474 94.820401 4.0315263 -1151.9074 -1151.9074 6.0428264 -3455.7909 -5.9742178 2.5364733 791.3799 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7839 ave 7839 max 7839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74804 ave 74804 max 74804 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149608 ave 149608 max 149608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149608 Ave neighs/atom = 139.3 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.9662/numatoms.out 1074 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3836.49568044851-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3836.49568044851-1074*${isolated_atom_energy} variable adjusted_pe_metal equal -3836.49568044851-1074*-9.5367431640625e-07 print "${adjusted_pe_metal} eV" file output/dump_039.9662/energy.out -3836.49465620229 eV print "${mindist_metal} Angstroms" file output/dump_039.9662/mindistance.out 2.53647328650029 Angstroms write_dump all cfg output/dump_039.9662/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_039.9662/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01