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 70.31214727586931*${_u_distance} variable xmax_converted equal 70.31214727586931*1 variable ymin_converted equal -70.3162761473251*${_u_distance} variable ymin_converted equal -70.3162761473251*1 variable ymax_converted equal 70.3162761473251*${_u_distance} variable ymax_converted equal 70.3162761473251*1 variable zmin_converted equal 0.0*${_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 70.3121472758693 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 70.3121472758693 -70.3162761473251 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 70.3121472758693 -70.3162761473251 70.3162761473251 ${zmin_converted} ${zmax_converted} units box region whole block 0 70.3121472758693 -70.3162761473251 70.3162761473251 0 ${zmax_converted} units box region whole block 0 70.3121472758693 -70.3162761473251 70.3162761473251 0 4.12887145578861 units box create_box 2 whole Created orthogonal box = (0 -70.3163 0) to (70.3121 70.3163 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 70.3162761473251 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.81894 5.81894 4.12887 create_atoms 1 region upper Created 1161 atoms create_atoms CPU = 0.000306129 secs group upper type 1 1161 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.663223864666881 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -70.3162761473251 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 lattice fcc 4.12887145578861 orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.81894 5.81894 4.12887 create_atoms 2 region lower Created 1161 atoms create_atoms CPU = 0.000200987 secs group lower type 2 1161 atoms in group lower displace_atoms lower move -7.663223864666881 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 16 31 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 31 atoms, new total = 2291 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 = 16 31 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) = 10.36 | 10.36 | 10.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8467.7249 0 -8467.7249 -7422.5313 326 0 -8493.0675 0 -8493.0675 -10784.107 Loop time of 9.77667 on 1 procs for 326 steps with 2291 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 = -8467.72493607 -8493.06746419 -8493.06746419 Force two-norm initial, final = 13.8495 3.27247e-05 Force max component initial, final = 3.25397 5.4467e-06 Final line search alpha, max atom move = 1 5.4467e-06 Iterations, force evaluations = 326 631 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6578 | 9.6578 | 9.6578 | 0.0 | 98.78 Neigh | 0.031091 | 0.031091 | 0.031091 | 0.0 | 0.32 Comm | 0.05722 | 0.05722 | 0.05722 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03057 | | | 0.31 Nlocal: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15522 ave 15522 max 15522 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: 407636 ave 407636 max 407636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407636 Ave neighs/atom = 177.929 Neighbor list builds = 3 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) = 10.36 | 10.36 | 10.36 Mbytes Step Temp E_pair E_mol TotEng Press Volume 326 0 -8493.0675 0 -8493.0675 -10784.107 40827.011 1326 0 -8494.1615 0 -8494.1615 -1864.8695 40465.502 Loop time of 30.6439 on 1 procs for 1000 steps with 2291 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 = -8493.06746419 -8494.1615087 -8494.16150892 Force two-norm initial, final = 347.179 0.0838245 Force max component initial, final = 251.926 0.0606434 Final line search alpha, max atom move = 0.0241654 0.00146547 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.005 | 30.005 | 30.005 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1409 | 0.1409 | 0.1409 | 0.0 | 0.46 Output | 6.6042e-05 | 6.6042e-05 | 6.6042e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4977 | | | 1.62 Nlocal: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14044 ave 14044 max 14044 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: 406846 ave 406846 max 406846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406846 Ave neighs/atom = 177.584 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 = 16 31 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) = 9.862 | 9.862 | 9.862 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8494.1615 0 -8494.1615 -1864.8695 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2291 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: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14074 ave 14074 max 14074 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: 413588 ave 413588 max 413588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413588 Ave neighs/atom = 180.527 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) = 9.862 | 9.862 | 9.862 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 -8494.1615 -8494.1615 70.000894 140.63255 4.1105079 -1864.8695 -1864.8695 2.3904645 -5597.6412 0.6422861 2.5202244 752.61946 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2291 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: 2291 ave 2291 max 2291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14074 ave 14074 max 14074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206794 ave 206794 max 206794 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 413588 ave 413588 max 413588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413588 Ave neighs/atom = 180.527 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_080.4727/numatoms.out 2291 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8494.16150891869-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8494.16150891869-2291*${isolated_atom_energy} variable adjusted_pe_metal equal -8494.16150891869-2291*0 print "${adjusted_pe_metal} eV" file output/dump_080.4727/energy.out -8494.16150891869 eV print "${mindist_metal} Angstroms" file output/dump_080.4727/mindistance.out 2.52022441629684 Angstroms write_dump all cfg output/dump_080.4727/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_080.4727/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:40