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 4.051526293158533*${_u_distance} variable lattice_constant_converted equal 4.051526293158533*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 68.99500661790626*${_u_distance} variable xmax_converted equal 68.99500661790626*1 variable ymin_converted equal -68.99905814419941*${_u_distance} variable ymin_converted equal -68.99905814419941*1 variable ymax_converted equal 68.99905814419941*${_u_distance} variable ymax_converted equal 68.99905814419941*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.051526293158533*${_u_distance} variable zmax_converted equal 4.051526293158533*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05152629315853 Lattice spacing in x,y,z = 4.05153 4.05153 4.05153 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 68.9950066179063 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.9950066179063 -68.9990581441994 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.9950066179063 -68.9990581441994 68.9990581441994 ${zmin_converted} ${zmax_converted} units box region whole block 0 68.9950066179063 -68.9990581441994 68.9990581441994 0 ${zmax_converted} units box region whole block 0 68.9950066179063 -68.9990581441994 68.9990581441994 0 4.05152629315853 units box create_box 2 whole Created orthogonal box = (0 -68.9991 0) to (68.995 68.9991 4.05153) 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 68.9990581441994 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 13 -11 0 orient y 11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70993 5.70993 4.05153 create_atoms 1 region upper Created 1162 atoms create_atoms CPU = 0.000452042 secs group upper type 1 1162 atoms in group upper mass 1 26.981538*${_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 -68.9990581441994 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 13 11 0 orient y -11 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70993 5.70993 4.05153 create_atoms 2 region lower Created 1162 atoms create_atoms CPU = 0.000343084 secs group lower type 2 1162 atoms in group lower displace_atoms lower move -7.663223864666881 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005 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*4.05152629315853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02576314657927 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 18 35 2 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 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2292 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 18 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.06 | 6.06 | 6.06 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7648.1001 0 -7648.1001 3018.6312 351 0 -7680.3631 0 -7680.3631 -4907.5385 Loop time of 4.71871 on 1 procs for 351 steps with 2292 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 = -7648.10011488 -7680.36306779 -7680.36306779 Force two-norm initial, final = 46.256 3.8551e-06 Force max component initial, final = 12.5769 5.05421e-07 Final line search alpha, max atom move = 1 5.05421e-07 Iterations, force evaluations = 351 697 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6241 | 4.6241 | 4.6241 | 0.0 | 98.00 Neigh | 0.0080121 | 0.0080121 | 0.0080121 | 0.0 | 0.17 Comm | 0.052477 | 0.052477 | 0.052477 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03411 | | | 0.72 Nlocal: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13383 ave 13383 max 13383 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: 304704 ave 304704 max 304704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304704 Ave neighs/atom = 132.942 Neighbor list builds = 1 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) = 6.06 | 6.06 | 6.06 Mbytes Step Temp E_pair E_mol TotEng Press Volume 351 0 -7680.3631 0 -7680.3631 -4907.5385 38575.315 1351 0 -7680.5206 0 -7680.5206 -2086.4212 38462.683 Loop time of 13.4671 on 1 procs for 1000 steps with 2292 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 = -7680.36306779 -7680.52063441 -7680.52063448 Force two-norm initial, final = 111.249 0.0470285 Force max component initial, final = 101.565 0.0339667 Final line search alpha, max atom move = 0.126919 0.00431103 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.841 | 12.841 | 12.841 | 0.0 | 95.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13623 | 0.13623 | 0.13623 | 0.0 | 1.01 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4895 | | | 3.63 Nlocal: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13393 ave 13393 max 13393 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: 304928 ave 304928 max 304928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304928 Ave neighs/atom = 133.04 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 -9.23201098901316e-12 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 18 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 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) = 6.198 | 6.198 | 6.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7680.5206 0 -7680.5206 -2086.4212 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2292 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: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13393 ave 13393 max 13393 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: 304960 ave 304960 max 304960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304960 Ave neighs/atom = 133.054 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) = 6.198 | 6.198 | 6.198 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 -7680.5206 -7680.5206 69.017024 137.99812 4.038408 -2086.4212 -2086.4212 -0.78511755 -6257.0683 -1.4103141 2.5792662 712.9914 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2292 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: 2292 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13393 ave 13393 max 13393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152480 ave 152480 max 152480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 304960 ave 304960 max 304960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304960 Ave neighs/atom = 133.054 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_080.4727/numatoms.out 2292 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7680.52063448197-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7680.52063448197-2292*${isolated_atom_energy} variable adjusted_pe_metal equal -7680.52063448197-2292*-9.23201098901316e-12 print "${adjusted_pe_metal} eV" file output/dump_080.4727/energy.out -7680.52063446081 eV print "${mindist_metal} Angstroms" file output/dump_080.4727/mindistance.out 2.57926623374378 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: 0:00:18