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 4.049998886883259*${_u_distance} variable lattice_constant_converted equal 4.049998886883259*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.20756187896994*${_u_distance} variable xmax_converted equal 60.20756187896994*1 variable ymin_converted equal -60.211611877856825*${_u_distance} variable ymin_converted equal -60.211611877856825*1 variable ymax_converted equal 60.211611877856825*${_u_distance} variable ymax_converted equal 60.211611877856825*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049998886883259*${_u_distance} variable zmax_converted equal 4.049998886883259*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999888688326 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 60.2075618789699 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2075618789699 -60.2116118778568 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2075618789699 -60.2116118778568 60.2116118778568 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2075618789699 -60.2116118778568 60.2116118778568 0 ${zmax_converted} units box region whole block 0 60.2075618789699 -60.2116118778568 60.2116118778568 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -60.2116 0) to (60.2076 60.2116 4.05) 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 60.2116118778568 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -10 0 orient y 10 11 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 11 -10 0 orient y 10 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72108 5.72108 4.05 create_atoms 1 region upper Created 885 atoms create_atoms CPU = 0.000271082 secs group upper type 1 885 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.689730936293327 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.2116118778568 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 10 0 orient y -10 11 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 11 10 0 orient y -10 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72108 5.72108 4.05 create_atoms 2 region lower Created 885 atoms create_atoms CPU = 0.000161171 secs group lower type 2 885 atoms in group lower displace_atoms lower move -6.689730936293327 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_811588957187_000-files/b'library-Al.meam' Al ./SM_811588957187_000-files/b'Al.meam' 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*4.04999888688326 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499944344163 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 ghost atom cutoff = 7 binsize = 3.5, bins = 18 35 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 26 atoms, new total = 1744 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 ghost atom cutoff = 7 binsize = 3.5, bins = 18 35 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5809.8283 0 -5809.8283 3468.8131 329 0 -5846.0313 0 -5846.0313 -6473.5583 Loop time of 11.4432 on 1 procs for 329 steps with 1744 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 = -5809.82832479 -5846.03129017 -5846.03129017 Force two-norm initial, final = 42.3604 2.7732e-05 Force max component initial, final = 8.6844 7.21965e-06 Final line search alpha, max atom move = 1 7.21965e-06 Iterations, force evaluations = 329 651 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.379 | 11.379 | 11.379 | 0.0 | 99.44 Neigh | 0.0049741 | 0.0049741 | 0.0049741 | 0.0 | 0.04 Comm | 0.03479 | 0.03479 | 0.03479 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02457 | | | 0.21 Nlocal: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949 ave 8949 max 8949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68642 ave 68642 max 68642 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137284 ave 137284 max 137284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137284 Ave neighs/atom = 78.7179 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) = 13.89 | 13.89 | 13.89 Mbytes Step Temp E_pair E_mol TotEng Press Volume 329 0 -5846.0313 0 -5846.0313 -6473.5583 29364.066 1329 0 -5846.2712 0 -5846.2712 -2736.0881 29215.422 Loop time of 38.1786 on 1 procs for 1000 steps with 1744 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 = -5846.03129017 -5846.27123386 -5846.27123387 Force two-norm initial, final = 111.399 0.0170069 Force max component initial, final = 95.77 0.0135796 Final line search alpha, max atom move = 0.20958 0.00284602 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.728 | 37.728 | 37.728 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.097196 | 0.097196 | 0.097196 | 0.0 | 0.25 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3532 | | | 0.93 Nlocal: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8902 ave 8902 max 8902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68840 ave 68840 max 68840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137680 ave 137680 max 137680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137680 Ave neighs/atom = 78.945 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 18 35 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 12.79 | 12.79 | 12.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5846.2712 0 -5846.2712 -2736.0881 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1744 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: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8954 ave 8954 max 8954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69788 ave 69788 max 69788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139576 ave 139576 max 139576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139576 Ave neighs/atom = 80.0321 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) = 12.79 | 12.79 | 12.79 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 -5846.2712 -5846.2712 60.195107 120.42322 4.030331 -2736.0881 -2736.0881 -0.52946852 -8206.9937 -0.74109205 2.5494409 292.54198 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1744 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: 1744 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8954 ave 8954 max 8954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69788 ave 69788 max 69788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139576 ave 139576 max 139576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139576 Ave neighs/atom = 80.0321 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_084.5474/numatoms.out 1744 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5846.27123386932-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5846.27123386932-1744*${isolated_atom_energy} variable adjusted_pe_metal equal -5846.27123386932-1744*0 print "${adjusted_pe_metal} eV" file output/dump_084.5474/energy.out -5846.27123386932 eV print "${mindist_metal} Angstroms" file output/dump_084.5474/mindistance.out 2.54944087570547 Angstroms write_dump all cfg output/dump_084.5474/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_084.5474/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:49