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 4.039798453450203*${_u_distance} variable lattice_constant_converted equal 4.039798453450203*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 50.6185295369817*${_u_distance} variable xmax_converted equal 50.6185295369817*1 variable ymin_converted equal -50.622569335435145*${_u_distance} variable ymin_converted equal -50.622569335435145*1 variable ymax_converted equal 50.622569335435145*${_u_distance} variable ymax_converted equal 50.622569335435145*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.039798453450203*${_u_distance} variable zmax_converted equal 4.039798453450203*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0397984534502 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 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 50.6185295369817 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 50.6185295369817 -50.6225693354351 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 50.6185295369817 -50.6225693354351 50.6225693354351 ${zmin_converted} ${zmax_converted} units box region whole block 0 50.6185295369817 -50.6225693354351 50.6225693354351 0 ${zmax_converted} units box region whole block 0 50.6185295369817 -50.6225693354351 50.6225693354351 0 4.0397984534502 units box create_box 2 whole Created orthogonal box = (0 -50.6226 0) to (50.6185 50.6226 4.0398) 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 50.6225693354351 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -6 0 orient y 6 11 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 11 -6 0 orient y 6 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48099 5.48099 4.0398 create_atoms 1 region upper Created 630 atoms create_atoms CPU = 0.000242949 secs group upper type 1 630 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.63848383876375 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -50.6225693354351 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 6 0 orient y -6 11 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 11 6 0 orient y -6 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48099 5.48099 4.0398 create_atoms 2 region lower Created 630 atoms create_atoms CPU = 0.000115156 secs group lower type 2 630 atoms in group lower displace_atoms lower move -5.63848383876375 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Al__MO_279544746097_002 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*4.0397984534502 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0198992267251 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1238 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.711 | 6.711 | 6.711 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3507.6182 0 -3507.6182 1553.4268 716 0 -3549.5023 0 -3549.5023 -7155.2531 Loop time of 16.0903 on 1 procs for 716 steps with 1238 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3507.6182452 -3549.50225028 -3549.50225028 Force two-norm initial, final = 29.438 2.86737e-05 Force max component initial, final = 5.31413 5.33636e-06 Final line search alpha, max atom move = 1 5.33636e-06 Iterations, force evaluations = 716 1414 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.91 | 15.91 | 15.91 | 0.0 | 98.88 Neigh | 0.019323 | 0.019323 | 0.019323 | 0.0 | 0.12 Comm | 0.11546 | 0.11546 | 0.11546 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04577 | | | 0.28 Nlocal: 1238 ave 1238 max 1238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14386 ave 14386 max 14386 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: 487672 ave 487672 max 487672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487672 Ave neighs/atom = 393.919 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) = 6.711 | 6.711 | 6.711 Mbytes Step Temp E_pair E_mol TotEng Press Volume 716 0 -3549.5023 0 -3549.5023 -7155.2531 20703.482 1716 0 -3549.7624 0 -3549.7624 -2525.0888 20572.69 Loop time of 23.6084 on 1 procs for 1000 steps with 1238 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 = -3549.50225028 -3549.76242181 -3549.7624219 Force two-norm initial, final = 102.319 0.0353694 Force max component initial, final = 84.6774 0.0319789 Final line search alpha, max atom move = 0.109717 0.00350863 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.995 | 22.995 | 22.995 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15063 | 0.15063 | 0.15063 | 0.0 | 0.64 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4628 | | | 1.96 Nlocal: 1238 ave 1238 max 1238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14386 ave 14386 max 14386 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: 482328 ave 482328 max 482328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482328 Ave neighs/atom = 389.603 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 6.85 | 6.85 | 6.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3549.7624 0 -3549.7624 -2525.0888 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1238 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: 1238 ave 1238 max 1238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14435 ave 14435 max 14435 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: 496404 ave 496404 max 496404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496404 Ave neighs/atom = 400.973 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) = 6.85 | 6.85 | 6.85 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 -3549.7624 -3549.7624 50.289181 101.24514 4.0405672 -2525.0888 -2525.0888 2.4742719 -7578.4961 0.75530245 2.5298522 713.06131 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1238 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: 1238 ave 1238 max 1238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14435 ave 14435 max 14435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 248202 ave 248202 max 248202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 496404 ave 496404 max 496404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496404 Ave neighs/atom = 400.973 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_057.2209/numatoms.out 1238 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3549.76242189568-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3549.76242189568-1238*${isolated_atom_energy} variable adjusted_pe_metal equal -3549.76242189568-1238*0 print "${adjusted_pe_metal} eV" file output/dump_057.2209/energy.out -3549.76242189568 eV print "${mindist_metal} Angstroms" file output/dump_057.2209/mindistance.out 2.52985215785585 Angstroms write_dump all cfg output/dump_057.2209/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_057.2209/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:39