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 4.128871455788613*${_u_distance} variable lattice_constant_converted equal 4.128871455788613*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 57.360115439181385*${_u_distance} variable xmax_converted equal 57.360115439181385*1 variable ymin_converted equal -57.364244310637176*${_u_distance} variable ymin_converted equal -57.364244310637176*1 variable ymax_converted equal 57.364244310637176*${_u_distance} variable ymax_converted equal 57.364244310637176*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.128871455788613*${_u_distance} variable zmax_converted equal 4.128871455788613*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.12887145578861 Lattice spacing in x,y,z = 4.12887 4.12887 4.12887 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 57.3601154391814 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.3601154391814 -57.3642443106372 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.3601154391814 -57.3642443106372 57.3642443106372 ${zmin_converted} ${zmax_converted} units box region whole block 0 57.3601154391814 -57.3642443106372 57.3642443106372 0 ${zmax_converted} units box region whole block 0 57.3601154391814 -57.3642443106372 57.3642443106372 0 4.12887145578861 units box create_box 2 whole Created orthogonal box = (0 -57.3642 0) to (57.3601 57.3642 4.12887) 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 57.3642443106372 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 12 -7 0 orient y 7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64685 5.64685 4.12887 create_atoms 1 region upper Created 774 atoms create_atoms CPU = 0.000246048 secs group upper type 1 774 atoms in group upper mass 1 26.981538*${_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 -57.3642443106372 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 12 7 0 orient y -7 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64685 5.64685 4.12887 create_atoms 2 region lower Created 774 atoms create_atoms CPU = 0.000138998 secs group lower type 2 774 atoms in group lower displace_atoms lower move -6.251599795252412 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_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*4.12887145578861 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0644357278943 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, 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 9.2 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 13 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.547 | 5.547 | 5.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5622.7649 0 -5622.7649 -6989.5639 252 0 -5645.3549 0 -5645.3549 -10448.171 Loop time of 4.93327 on 1 procs for 252 steps with 1524 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 = -5622.76492079 -5645.35485101 -5645.35485101 Force two-norm initial, final = 21.4164 2.5042e-05 Force max component initial, final = 4.92322 2.92729e-06 Final line search alpha, max atom move = 1 2.92729e-06 Iterations, force evaluations = 252 495 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8849 | 4.8849 | 4.8849 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.031608 | 0.031608 | 0.031608 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01671 | | | 0.34 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11249 ave 11249 max 11249 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: 265768 ave 265768 max 265768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 265768 Ave neighs/atom = 174.388 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) = 5.547 | 5.547 | 5.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 252 0 -5645.3549 0 -5645.3549 -10448.171 27171.44 1252 0 -5646.1195 0 -5646.1195 -1405.606 26926.297 Loop time of 21.4016 on 1 procs for 1000 steps with 1524 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5645.35485101 -5646.11953839 -5646.11953855 Force two-norm initial, final = 234.953 0.057275 Force max component initial, final = 175.693 0.0284967 Final line search alpha, max atom move = 0.026425 0.000753024 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.93 | 20.93 | 20.93 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10472 | 0.10472 | 0.10472 | 0.0 | 0.49 Output | 2.1935e-05 | 2.1935e-05 | 2.1935e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3666 | | | 1.71 Nlocal: 1524 ave 1524 max 1524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10156 ave 10156 max 10156 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: 270108 ave 270108 max 270108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270108 Ave neighs/atom = 177.236 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 13 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.677 | 5.677 | 5.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5646.1195 0 -5646.1195 -1405.606 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: 10176 ave 10176 max 10176 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: 277120 ave 277120 max 277120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 277120 Ave neighs/atom = 181.837 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) = 5.677 | 5.677 | 5.677 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 -5646.1195 -5646.1195 57.044417 114.72849 4.1142645 -1405.606 -1405.606 1.6862844 -4219.7683 1.2639398 2.5811482 957.32687 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: 10176 ave 10176 max 10176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 138560 ave 138560 max 138560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 277120 ave 277120 max 277120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 277120 Ave neighs/atom = 181.837 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -5646.11953855299-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5646.11953855299-1524*${isolated_atom_energy} variable adjusted_pe_metal equal -5646.11953855299-1524*0 print "${adjusted_pe_metal} eV" file output/dump_060.5129/energy.out -5646.11953855299 eV print "${mindist_metal} Angstroms" file output/dump_060.5129/mindistance.out 2.5811482374226 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: 0:00:26