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 47.40402160971706*${_u_distance} variable xmax_converted equal 47.40402160971706*1 variable ymin_converted equal -47.40807160860395*${_u_distance} variable ymin_converted equal -47.40807160860395*1 variable ymax_converted equal 47.40807160860395*${_u_distance} variable ymax_converted equal 47.40807160860395*1 variable zmin_converted equal 0.0*${_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 47.4040216097171 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4040216097171 -47.4080716086039 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4040216097171 -47.4080716086039 47.4080716086039 ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4040216097171 -47.4080716086039 47.4080716086039 0 ${zmax_converted} units box region whole block 0 47.4040216097171 -47.4080716086039 47.4080716086039 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -47.4081 0) to (47.404 47.4081 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 47.4080716086039 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.19022 5.19022 4.05 create_atoms 1 region upper Created 550 atoms create_atoms CPU = 0.000209093 secs group upper type 1 550 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.267114959823831 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -47.4080716086039 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.19022 5.19022 4.05 create_atoms 2 region lower Created 550 atoms create_atoms CPU = 9.70364e-05 secs group lower type 2 550 atoms in group lower displace_atoms lower move -5.267114959823831 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_721930391003_000-files/b'AlU-library.meam' Al U ./SM_721930391003_000-files/b'AlU.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 = 14 28 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 = 1074 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 = 14 28 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) = 12.13 | 12.13 | 12.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3567.4298 0 -3567.4298 2807.6388 328 0 -3591.2972 0 -3591.2972 -7156.5137 Loop time of 7.12643 on 1 procs for 328 steps with 1074 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3567.4297628 -3591.29723257 -3591.29723257 Force two-norm initial, final = 23.7665 1.02945e-05 Force max component initial, final = 6.81958 2.08639e-06 Final line search alpha, max atom move = 1 2.08639e-06 Iterations, force evaluations = 328 646 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0809 | 7.0809 | 7.0809 | 0.0 | 99.36 Neigh | 0.0053186 | 0.0053186 | 0.0053186 | 0.0 | 0.07 Comm | 0.023549 | 0.023549 | 0.023549 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01668 | | | 0.23 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6066 ave 6066 max 6066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42074 ave 42074 max 42074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84148 ave 84148 max 84148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84148 Ave neighs/atom = 78.3501 Neighbor list builds = 2 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) = 12.15 | 12.15 | 12.15 Mbytes Step Temp E_pair E_mol TotEng Press Volume 328 0 -3591.2972 0 -3591.2972 -7156.5137 18203.394 1328 0 -3591.5632 0 -3591.5632 -1766.303 18068.157 Loop time of 22.1871 on 1 procs for 1000 steps with 1074 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 = -3591.29723257 -3591.5631894 -3591.56318942 Force two-norm initial, final = 98.6988 0.00851011 Force max component initial, final = 73.9522 0.00655404 Final line search alpha, max atom move = 0.204031 0.00133723 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.887 | 21.887 | 21.887 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.064707 | 0.064707 | 0.064707 | 0.0 | 0.29 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2349 | | | 1.06 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6058 ave 6058 max 6058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42134 ave 42134 max 42134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84268 ave 84268 max 84268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84268 Ave neighs/atom = 78.4618 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 = 14 28 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) = 11.05 | 11.05 | 11.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3591.5632 0 -3591.5632 -1766.303 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6083 ave 6083 max 6083 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43234 ave 43234 max 43234 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86468 ave 86468 max 86468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86468 Ave neighs/atom = 80.5102 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) = 11.05 | 11.05 | 11.05 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 -3591.5632 -3591.5632 47.279892 94.816143 4.0304645 -1766.303 -1766.303 -0.57965104 -5298.3068 -0.022375055 2.4764215 800.73349 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1074 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 | | 1.192e-06 | | |100.00 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6083 ave 6083 max 6083 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43234 ave 43234 max 43234 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86468 ave 86468 max 86468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86468 Ave neighs/atom = 80.5102 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.9662/numatoms.out 1074 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3591.56318942248-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3591.56318942248-1074*${isolated_atom_energy} variable adjusted_pe_metal equal -3591.56318942248-1074*0 print "${adjusted_pe_metal} eV" file output/dump_039.9662/energy.out -3591.56318942248 eV print "${mindist_metal} Angstroms" file output/dump_039.9662/mindistance.out 2.47642153683831 Angstroms write_dump all cfg output/dump_039.9662/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_039.9662/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:29