LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 61.560897742830086*${_u_distance} variable xmax_converted equal 61.560897742830086*1 variable ymin_converted equal -61.56493073133366*${_u_distance} variable ymin_converted equal -61.56493073133366*1 variable ymax_converted equal 61.56493073133366*${_u_distance} variable ymax_converted equal 61.56493073133366*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 61.5608977428301 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.5608977428301 -61.5649307313337 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.5608977428301 -61.5649307313337 61.5649307313337 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.5608977428301 -61.5649307313337 61.5649307313337 0 ${zmax_converted} units box region whole block 0 61.5608977428301 -61.5649307313337 61.5649307313337 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -61.5649 0) to (61.5609 61.5649 4.03299) 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 61.5649307313337 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.54841 5.54841 4.03299 create_atoms 1 region upper Created 933 atoms create_atoms CPU = 0.00027585 secs group upper type 1 933 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.868951885113186 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.5649307313337 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.54841 5.54841 4.03299 create_atoms 2 region lower Created 933 atoms create_atoms CPU = 0.000172853 secs group lower type 2 933 atoms in group lower displace_atoms lower move -6.868951885113186 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 9 18 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1840 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.5 | 13.5 | 13.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5289.5741 0 -5289.5741 1335.2105 448 0 -5349.6127 0 -5349.6127 -7055.0862 Loop time of 20.4916 on 1 procs for 448 steps with 1840 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 = -5289.57407842 -5349.61268734 -5349.61268734 Force two-norm initial, final = 33.9489 2.03498e-05 Force max component initial, final = 6.66726 3.4137e-06 Final line search alpha, max atom move = 1 3.4137e-06 Iterations, force evaluations = 448 855 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.281 | 20.281 | 20.281 | 0.0 | 98.97 Neigh | 0.08172 | 0.08172 | 0.08172 | 0.0 | 0.40 Comm | 0.096849 | 0.096849 | 0.096849 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03176 | | | 0.15 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24200 ave 24200 max 24200 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: 1.2133e+06 ave 1.2133e+06 max 1.2133e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1213304 Ave neighs/atom = 659.404 Neighbor list builds = 4 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) = 13.5 | 13.5 | 13.5 Mbytes Step Temp E_pair E_mol TotEng Press Volume 448 0 -5349.6127 0 -5349.6127 -7055.0862 30569.992 1448 0 -5349.9127 0 -5349.9127 -2690.4631 30387.381 Loop time of 49.3429 on 1 procs for 1000 steps with 1840 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5349.61268734 -5349.91266773 -5349.91266939 Force two-norm initial, final = 138.769 0.25657 Force max component initial, final = 107.76 0.256393 Final line search alpha, max atom move = 0.00921374 0.00236234 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 48.564 | 48.564 | 48.564 | 0.0 | 98.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.21458 | 0.21458 | 0.21458 | 0.0 | 0.43 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5639 | | | 1.14 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24192 ave 24192 max 24192 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: 1.20928e+06 ave 1.20928e+06 max 1.20928e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1209280 Ave neighs/atom = 657.217 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 13.01 | 13.01 | 13.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5349.9127 0 -5349.9127 -2690.4631 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24184 ave 24184 max 24184 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: 1.21383e+06 ave 1.21383e+06 max 1.21383e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1213832 Ave neighs/atom = 659.691 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:52) Per MPI rank memory allocation (min/avg/max) = 13.01 | 13.01 | 13.01 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 -5349.9127 -5349.9127 61.340485 123.12986 4.0233024 -2690.4631 -2690.4631 -13.469929 -8058.2145 0.29518884 2.5160788 769.78028 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 24184 ave 24184 max 24184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 606916 ave 606916 max 606916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.21383e+06 ave 1.21383e+06 max 1.21383e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1213832 Ave neighs/atom = 659.691 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_063.2150/numatoms.out 1840 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5349.91266939298-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5349.91266939298-1840*${isolated_atom_energy} variable adjusted_pe_metal equal -5349.91266939298-1840*0 print "${adjusted_pe_metal} eV" file output/dump_063.2150/energy.out -5349.91266939298 eV print "${mindist_metal} Angstroms" file output/dump_063.2150/mindistance.out 2.51607884039398 Angstroms write_dump all cfg output/dump_063.2150/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_063.2150/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:10