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 37.182316804463824*${_u_distance} variable xmax_converted equal 37.182316804463824*1 variable ymin_converted equal -74.36866659743123*${_u_distance} variable ymin_converted equal -74.36866659743123*1 variable ymax_converted equal 74.36866659743123*${_u_distance} variable ymax_converted equal 74.36866659743123*1 variable zmin_converted equal 0.0*${_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 37.1823168044638 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.1823168044638 -74.3686665974312 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.1823168044638 -74.3686665974312 74.3686665974312 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.1823168044638 -74.3686665974312 74.3686665974312 0 ${zmax_converted} units box region whole block 0 37.1823168044638 -74.3686665974312 74.3686665974312 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -74.3687 0) to (37.1823 74.3687 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 74.3686665974312 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -6 0 orient y 6 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 -6 0 orient y 6 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68671 5.68671 4.03299 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000250101 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.3686665974312 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 6 0 orient y -6 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 6 0 orient y -6 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68671 5.68671 4.03299 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.00016284 secs group lower type 2 682 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 6 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1352 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 = 6 22 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) = 12.25 | 12.25 | 12.25 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3899.366 0 -3899.366 3640.8505 413 0 -3943.7146 0 -3943.7146 -3489.4749 Loop time of 14.5622 on 1 procs for 413 steps with 1352 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 = -3899.36596928 -3943.71462346 -3943.71462346 Force two-norm initial, final = 36.8413 2.8442e-06 Force max component initial, final = 7.12558 4.04492e-07 Final line search alpha, max atom move = 1 4.04492e-07 Iterations, force evaluations = 413 817 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.46 | 14.46 | 14.46 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079128 | 0.079128 | 0.079128 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02348 | | | 0.16 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20920 ave 20920 max 20920 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: 904468 ave 904468 max 904468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 904468 Ave neighs/atom = 668.985 Neighbor list builds = 0 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) = 12.25 | 12.25 | 12.25 Mbytes Step Temp E_pair E_mol TotEng Press Volume 413 0 -3943.7146 0 -3943.7146 -3489.4749 22304.034 1413 0 -3943.7422 0 -3943.7422 -1890.5481 22255.536 Loop time of 36.6161 on 1 procs for 1000 steps with 1352 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 = -3943.71462346 -3943.74215111 -3943.74215111 Force two-norm initial, final = 35.5537 0.0024522 Force max component initial, final = 25.2249 0.00149373 Final line search alpha, max atom move = 1 0.00149373 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.956 | 35.956 | 35.956 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.185 | 0.185 | 0.185 | 0.0 | 0.51 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4753 | | | 1.30 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20880 ave 20880 max 20880 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: 898120 ave 898120 max 898120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 898120 Ave neighs/atom = 664.29 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 = 6 22 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) = 11.77 | 11.77 | 11.77 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3943.7422 0 -3943.7422 -1890.5481 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20880 ave 20880 max 20880 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: 899464 ave 899464 max 899464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 899464 Ave neighs/atom = 665.284 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) = 11.77 | 11.77 | 11.77 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 -3943.7422 -3943.7422 37.163187 148.73733 4.0262906 -1890.5481 -1890.5481 0.107478 -5671.7375 -0.014171986 2.5530359 183.31321 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20880 ave 20880 max 20880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 449732 ave 449732 max 449732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 899464 ave 899464 max 899464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 899464 Ave neighs/atom = 665.284 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.2026/numatoms.out 1352 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3943.74215110925-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3943.74215110925-1352*${isolated_atom_energy} variable adjusted_pe_metal equal -3943.74215110925-1352*0 print "${adjusted_pe_metal} eV" file output/dump_081.2026/energy.out -3943.74215110925 eV print "${mindist_metal} Angstroms" file output/dump_081.2026/mindistance.out 2.55303593580232 Angstroms write_dump all cfg output/dump_081.2026/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_081.2026/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:51