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 4.050199627876282*${_u_distance} variable lattice_constant_converted equal 4.050199627876282*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 52.80814231120385*${_u_distance} variable xmax_converted equal 52.80814231120385*1 variable ymin_converted equal -52.81219251083173*${_u_distance} variable ymin_converted equal -52.81219251083173*1 variable ymax_converted equal 52.81219251083173*${_u_distance} variable ymax_converted equal 52.81219251083173*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050199627876282*${_u_distance} variable zmax_converted equal 4.050199627876282*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05019962787628 Lattice spacing in x,y,z = 4.0502 4.0502 4.0502 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 52.8081423112039 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.8081423112039 -52.8121925108317 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.8081423112039 -52.8121925108317 52.8121925108317 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.8081423112039 -52.8121925108317 52.8121925108317 0 ${zmax_converted} units box region whole block 0 52.8081423112039 -52.8121925108317 52.8121925108317 0 4.05019962787628 units box create_box 2 whole Created orthogonal box = (0 -52.8122 0) to (52.8081 52.8122 4.0502) 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 52.8121925108317 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 13 -1 0 orient y 1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.34891 4.34891 4.0502 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.00027895 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.867282164682384 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.8121925108317 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 lattice fcc 4.05019962787628 orient x 13 1 0 orient y -1 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.34891 4.34891 4.0502 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000149012 secs group lower type 2 682 atoms in group lower displace_atoms lower move -5.867282164682384 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Al__MO_060567868558_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*4.05019962787628 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02509981393814 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 = 13 26 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 24 atoms, new total = 1340 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 = 13 26 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) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4779.0566 0 -4779.0566 -2189.9311 89 0 -4790.5638 0 -4790.5638 -4490.9906 Loop time of 0.928395 on 1 procs for 89 steps with 1340 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4779.05659767 -4790.5637973 -4790.5637973 Force two-norm initial, final = 9.24454 0.00850482 Force max component initial, final = 1.98227 0.00101648 Final line search alpha, max atom move = 0.00012207 1.24081e-07 Iterations, force evaluations = 89 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9068 | 0.9068 | 0.9068 | 0.0 | 97.67 Neigh | 0.0052559 | 0.0052559 | 0.0052559 | 0.0 | 0.57 Comm | 0.010389 | 0.010389 | 0.010389 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005954 | | | 0.64 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8925 ave 8925 max 8925 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: 187668 ave 187668 max 187668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187668 Ave neighs/atom = 140.051 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) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -4790.5638 0 -4790.5638 -4490.9906 22591.315 101 0 -4790.6656 0 -4790.6656 -1529.6031 22501.68 Loop time of 0.233046 on 1 procs for 12 steps with 1340 atoms 103.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4790.5637973 -4790.66555631 -4790.66555631 Force two-norm initial, final = 65.597 0.110529 Force max component initial, final = 47.6751 0.101234 Final line search alpha, max atom move = 5.45665e-07 5.52399e-08 Iterations, force evaluations = 12 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22287 | 0.22287 | 0.22287 | 0.0 | 95.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023744 | 0.0023744 | 0.0023744 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007804 | | | 3.35 Nlocal: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8952 ave 8952 max 8952 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: 187748 ave 187748 max 187748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187748 Ave neighs/atom = 140.11 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 = 8.40393 ghost atom cutoff = 8.40393 binsize = 4.20196, bins = 13 26 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) = 5.229 | 5.229 | 5.229 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4790.6656 0 -4790.6656 -1529.6031 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8955 ave 8955 max 8955 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: 187928 ave 187928 max 187928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187928 Ave neighs/atom = 140.245 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) = 5.229 | 5.229 | 5.229 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 -4790.6656 -4790.6656 52.692841 105.62439 4.0429571 -1529.6031 -1529.6031 7.1923839 -4595.7698 -0.23184293 2.6337835 249.91929 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1340 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: 1340 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8955 ave 8955 max 8955 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93964 ave 93964 max 93964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187928 ave 187928 max 187928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187928 Ave neighs/atom = 140.245 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_008.7974/numatoms.out 1340 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4790.66555631491-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4790.66555631491-1340*${isolated_atom_energy} variable adjusted_pe_metal equal -4790.66555631491-1340*0 print "${adjusted_pe_metal} eV" file output/dump_008.7974/energy.out -4790.66555631491 eV print "${mindist_metal} Angstroms" file output/dump_008.7974/mindistance.out 2.63378349811244 Angstroms write_dump all cfg output/dump_008.7974/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_008.7974/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01