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 4.073718130588532*${_u_distance} variable lattice_constant_converted equal 4.073718130588532*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 56.593900958007346*${_u_distance} variable xmax_converted equal 56.593900958007346*1 variable ymin_converted equal -56.59797467613794*${_u_distance} variable ymin_converted equal -56.59797467613794*1 variable ymax_converted equal 56.59797467613794*${_u_distance} variable ymax_converted equal 56.59797467613794*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.073718130588532*${_u_distance} variable zmax_converted equal 4.073718130588532*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.07371813058853 Lattice spacing in x,y,z = 4.07372 4.07372 4.07372 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 56.5939009580073 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.5939009580073 -56.5979746761379 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.5939009580073 -56.5979746761379 56.5979746761379 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.5939009580073 -56.5979746761379 56.5979746761379 0 ${zmax_converted} units box region whole block 0 56.5939009580073 -56.5979746761379 56.5979746761379 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -56.598 0) to (56.5939 56.598 4.07372) 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 56.5979746761379 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57142 5.57142 4.07372 create_atoms 1 region upper Created 774 atoms create_atoms CPU = 0.000355959 secs group upper type 1 774 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.251599795252412 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.5979746761379 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57142 5.57142 4.07372 create_atoms 2 region lower Created 774 atoms create_atoms CPU = 0.000211 secs group lower type 2 774 atoms in group lower displace_atoms lower move -6.251599795252412 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_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*4.07371813058853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03685906529426 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 25 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1524 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.933 | 5.933 | 5.933 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4640.2979 0 -4640.2979 1133.0684 339 0 -4661.6057 0 -4661.6057 -3402.8402 Loop time of 6.31076 on 1 procs for 339 steps with 1524 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 = -4640.2979242 -4661.605674 -4661.605674 Force two-norm initial, final = 24.5766 2.68542e-06 Force max component initial, final = 5.77692 1.27874e-06 Final line search alpha, max atom move = 1 1.27874e-06 Iterations, force evaluations = 339 669 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2424 | 6.2424 | 6.2424 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.045146 | 0.045146 | 0.045146 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02322 | | | 0.37 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11360 ave 11360 max 11360 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: 300640 ave 300640 max 300640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300640 Ave neighs/atom = 197.27 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) = 5.946 | 5.946 | 5.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 339 0 -4661.6057 0 -4661.6057 -3402.8402 26097.054 1339 0 -4661.7416 0 -4661.7416 -860.34844 25958.627 Loop time of 18.3521 on 1 procs for 1000 steps with 1524 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 = -4661.605674 -4661.74161861 -4661.74161869 Force two-norm initial, final = 69.0297 0.024616 Force max component initial, final = 55.7553 0.0210799 Final line search alpha, max atom move = 0.245344 0.00517184 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.805 | 17.805 | 17.805 | 0.0 | 97.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13165 | 0.13165 | 0.13165 | 0.0 | 0.72 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.415 | | | 2.26 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582 ave 12582 max 12582 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: 301692 ave 301692 max 301692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301692 Ave neighs/atom = 197.961 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 0.143095413925774 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 6.084 | 6.084 | 6.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4661.7416 0 -4661.7416 -860.34844 Loop time of 0 on 1 procs for 0 steps with 1524 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 | | 0 | | | 0.00 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582 ave 12582 max 12582 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: 301960 ave 301960 max 301960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301960 Ave neighs/atom = 198.136 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) = 6.084 | 6.084 | 6.084 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 -4661.7416 -4661.7416 56.388767 113.19595 4.0668508 -860.34844 -860.34844 -1.2963441 -2580.3355 0.58649824 2.5586367 1000.941 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1524 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: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582 ave 12582 max 12582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150980 ave 150980 max 150980 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 301960 ave 301960 max 301960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 301960 Ave neighs/atom = 198.136 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_060.5129/numatoms.out 1524 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4661.74161868807-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4661.74161868807-1524*${isolated_atom_energy} variable adjusted_pe_metal equal -4661.74161868807-1524*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_060.5129/energy.out -4879.81902951095 eV print "${mindist_metal} Angstroms" file output/dump_060.5129/mindistance.out 2.55863672188383 Angstroms write_dump all cfg output/dump_060.5129/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_060.5129/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:24