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 4.061213478446007*${_u_distance} variable lattice_constant_converted equal 4.061213478446007*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 53.41692335514553*${_u_distance} variable xmax_converted equal 53.41692335514553*1 variable ymin_converted equal -53.42098456862397*${_u_distance} variable ymin_converted equal -53.42098456862397*1 variable ymax_converted equal 53.42098456862397*${_u_distance} variable ymax_converted equal 53.42098456862397*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.061213478446007*${_u_distance} variable zmax_converted equal 4.061213478446007*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06121347844601 Lattice spacing in x,y,z = 4.06121 4.06121 4.06121 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 53.4169233551455 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.4169233551455 -53.420984568624 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.4169233551455 -53.420984568624 53.420984568624 ${zmin_converted} ${zmax_converted} units box region whole block 0 53.4169233551455 -53.420984568624 53.420984568624 0 ${zmax_converted} units box region whole block 0 53.4169233551455 -53.420984568624 53.420984568624 0 4.06121347844601 units box create_box 2 whole Created orthogonal box = (0 -53.421 0) to (53.4169 53.421 4.06121) 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 53.420984568624 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.63153 4.63153 4.06121 create_atoms 1 region upper Created 694 atoms create_atoms CPU = 0.000205994 secs group upper type 1 694 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.918825897084657 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -53.420984568624 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.63153 4.63153 4.06121 create_atoms 2 region lower Created 694 atoms create_atoms CPU = 0.000124931 secs group lower type 2 694 atoms in group lower displace_atoms lower move -5.918825897084657 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Al__MO_411898953661_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.06121347844601 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03060673922301 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 22 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1364 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.898 | 5.898 | 5.898 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3625.5077 0 -3625.5077 377.03983 327 0 -3658.3539 0 -3658.3539 -6496.3906 Loop time of 4.71158 on 1 procs for 327 steps with 1364 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3625.50772442 -3658.35389171 -3658.35389171 Force two-norm initial, final = 22.7304 1.34119e-05 Force max component initial, final = 6.28095 1.80096e-06 Final line search alpha, max atom move = 1 1.80096e-06 Iterations, force evaluations = 327 639 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6337 | 4.6337 | 4.6337 | 0.0 | 98.35 Neigh | 0.014222 | 0.014222 | 0.014222 | 0.0 | 0.30 Comm | 0.043764 | 0.043764 | 0.043764 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01987 | | | 0.42 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11752 ave 11752 max 11752 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: 304932 ave 304932 max 304932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304932 Ave neighs/atom = 223.557 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 (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 5.898 | 5.898 | 5.898 Mbytes Step Temp E_pair E_mol TotEng Press Volume 327 0 -3658.3539 0 -3658.3539 -6496.3906 23178.033 1327 0 -3658.6081 0 -3658.6081 -1747.6811 23025.238 Loop time of 15.3622 on 1 procs for 1000 steps with 1364 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 = -3658.35389171 -3658.6080891 -3658.60808913 Force two-norm initial, final = 106.007 0.0181885 Force max component initial, final = 79.3592 0.011871 Final line search alpha, max atom move = 0.114076 0.0013542 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.843 | 14.843 | 14.843 | 0.0 | 96.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12466 | 0.12466 | 0.12466 | 0.0 | 0.81 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3943 | | | 2.57 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11756 ave 11756 max 11756 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: 304960 ave 304960 max 304960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304960 Ave neighs/atom = 223.578 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 6.036 | 6.036 | 6.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3658.6081 0 -3658.6081 -1747.6811 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11802 ave 11802 max 11802 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: 305364 ave 305364 max 305364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305364 Ave neighs/atom = 223.874 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) = 6.036 | 6.036 | 6.036 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 -3658.6081 -3658.6081 53.172473 106.84197 4.0529887 -1747.6811 -1747.6811 0.82224888 -5244.311 0.44543948 2.5304471 501.99629 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11802 ave 11802 max 11802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152682 ave 152682 max 152682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 305364 ave 305364 max 305364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305364 Ave neighs/atom = 223.874 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_017.4923/numatoms.out 1364 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3658.60808913285-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3658.60808913285-1364*${isolated_atom_energy} variable adjusted_pe_metal equal -3658.60808913285-1364*0 print "${adjusted_pe_metal} eV" file output/dump_017.4923/energy.out -3658.60808913285 eV print "${mindist_metal} Angstroms" file output/dump_017.4923/mindistance.out 2.53044708903361 Angstroms write_dump all cfg output/dump_017.4923/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_017.4923/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:20