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 49.07182916864503*${_u_distance} variable xmax_converted equal 49.07182916864503*1 variable ymin_converted equal -49.075890382123475*${_u_distance} variable ymin_converted equal -49.075890382123475*1 variable ymax_converted equal 49.075890382123475*${_u_distance} variable ymax_converted equal 49.075890382123475*1 variable zmin_converted equal 0.0*${_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 49.071829168645 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 49.071829168645 -49.0758903821235 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 49.071829168645 -49.0758903821235 49.0758903821235 ${zmin_converted} ${zmax_converted} units box region whole block 0 49.071829168645 -49.0758903821235 49.0758903821235 0 ${zmax_converted} units box region whole block 0 49.071829168645 -49.0758903821235 49.0758903821235 0 4.06121347844601 units box create_box 2 whole Created orthogonal box = (0 -49.0759 0) to (49.0718 49.0759 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 49.0758903821235 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -5 0 orient y 5 11 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 11 -5 0 orient y 5 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.37773 5.37773 4.06121 create_atoms 1 region upper Created 586 atoms create_atoms CPU = 0.000277042 secs group upper type 1 586 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.437370688117558 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -49.0758903821235 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 5 0 orient y -5 11 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 11 5 0 orient y -5 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.37773 5.37773 4.06121 create_atoms 2 region lower Created 586 atoms create_atoms CPU = 0.000160933 secs group lower type 2 586 atoms in group lower displace_atoms lower move -5.437370688117558 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 21 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 22 atoms, new total = 1150 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 21 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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3045.5064 0 -3045.5064 1232.5312 459 0 -3079.9142 0 -3079.9142 -6540.2301 Loop time of 5.43865 on 1 procs for 459 steps with 1150 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3045.50635653 -3079.91423676 -3079.91423676 Force two-norm initial, final = 26.2628 7.53723e-06 Force max component initial, final = 5.5951 1.17112e-06 Final line search alpha, max atom move = 1 1.17112e-06 Iterations, force evaluations = 459 896 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3473 | 5.3473 | 5.3473 | 0.0 | 98.32 Neigh | 0.013686 | 0.013686 | 0.013686 | 0.0 | 0.25 Comm | 0.053507 | 0.053507 | 0.053507 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02418 | | | 0.44 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10388 ave 10388 max 10388 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: 256548 ave 256548 max 256548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256548 Ave neighs/atom = 223.085 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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 459 0 -3079.9142 0 -3079.9142 -6540.2301 19560.784 1459 0 -3080.1409 0 -3080.1409 -1945.5254 19436.559 Loop time of 12.2391 on 1 procs for 1000 steps with 1150 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 = -3079.91423676 -3080.14090918 -3080.14091243 Force two-norm initial, final = 92.4766 0.12282 Force max component initial, final = 74.4179 0.0791011 Final line search alpha, max atom move = 0.0807044 0.00638381 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.8 | 11.8 | 11.8 | 0.0 | 96.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10721 | 0.10721 | 0.10721 | 0.0 | 0.88 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3314 | | | 2.71 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10412 ave 10412 max 10412 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: 256748 ave 256748 max 256748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256748 Ave neighs/atom = 223.259 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 = 10 21 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) = 5.599 | 5.599 | 5.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3080.1409 0 -3080.1409 -1945.5254 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1150 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: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10424 ave 10424 max 10424 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: 257076 ave 257076 max 257076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257076 Ave neighs/atom = 223.544 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) = 5.599 | 5.599 | 5.599 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 -3080.1409 -3080.1409 48.797045 98.151781 4.0581461 -1945.5254 -1945.5254 -6.483878 -5836.5312 6.4388706 2.5501048 768.87673 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1150 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 | | 1.192e-06 | | |100.00 Nlocal: 1150 ave 1150 max 1150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10424 ave 10424 max 10424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128538 ave 128538 max 128538 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257076 ave 257076 max 257076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257076 Ave neighs/atom = 223.544 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_048.8879/numatoms.out 1150 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3080.14091242741-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3080.14091242741-1150*${isolated_atom_energy} variable adjusted_pe_metal equal -3080.14091242741-1150*0 print "${adjusted_pe_metal} eV" file output/dump_048.8879/energy.out -3080.14091242741 eV print "${mindist_metal} Angstroms" file output/dump_048.8879/mindistance.out 2.55010478281725 Angstroms write_dump all cfg output/dump_048.8879/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_048.8879/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:17