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 37.33914478960691*${_u_distance} variable xmax_converted equal 37.33914478960691*1 variable ymin_converted equal -74.68233957810071*${_u_distance} variable ymin_converted equal -74.68233957810071*1 variable ymax_converted equal 74.68233957810071*${_u_distance} variable ymax_converted equal 74.68233957810071*1 variable zmin_converted equal 0.0*${_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 37.3391447896069 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 74.6823395781007 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 74.6823395781007 0 ${zmax_converted} units box region whole block 0 37.3391447896069 -74.6823395781007 74.6823395781007 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -74.6823 0) to (37.3391 74.6823 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 74.6823395781007 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -6 0 orient y 6 7 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 7 -6 0 orient y 6 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71069 5.71069 4.05 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000246048 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.6823395781007 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 6 0 orient y -6 7 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 7 6 0 orient y -6 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71069 5.71069 4.05 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000136137 secs group lower type 2 682 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 11 43 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 12 atoms, new total = 1352 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 = 11 43 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) = 13.16 | 13.16 | 13.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4490.3336 0 -4490.3336 8218.2252 354 0 -4535.6754 0 -4535.6754 -2296.3381 Loop time of 9.78481 on 1 procs for 354 steps with 1352 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4490.33363916 -4535.67542592 -4535.67542592 Force two-norm initial, final = 63.5423 1.73027e-05 Force max component initial, final = 13.388 2.72773e-06 Final line search alpha, max atom move = 1 2.72773e-06 Iterations, force evaluations = 354 702 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7307 | 9.7307 | 9.7307 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032485 | 0.032485 | 0.032485 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02165 | | | 0.22 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7770 ave 7770 max 7770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52620 ave 52620 max 52620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105240 ave 105240 max 105240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105240 Ave neighs/atom = 77.8402 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) = 13.18 | 13.18 | 13.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 354 0 -4535.6754 0 -4535.6754 -2296.3381 22587.449 1354 0 -4535.7015 0 -4535.7015 -749.14966 22541.85 Loop time of 27.342 on 1 procs for 1000 steps with 1352 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 = -4535.67542592 -4535.70146751 -4535.70146751 Force two-norm initial, final = 35.4673 0.00101025 Force max component initial, final = 26.9169 0.000531601 Final line search alpha, max atom move = 1 0.000531601 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.995 | 26.995 | 26.995 | 0.0 | 98.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.074449 | 0.074449 | 0.074449 | 0.0 | 0.27 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.273 | | | 1.00 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6756 ave 6756 max 6756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53288 ave 53288 max 53288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106576 ave 106576 max 106576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106576 Ave neighs/atom = 78.8284 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 = 11 43 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) = 12.05 | 12.05 | 12.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4535.7015 0 -4535.7015 -749.14966 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6756 ave 6756 max 6756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53432 ave 53432 max 53432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106864 ave 106864 max 106864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106864 Ave neighs/atom = 79.0414 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) = 12.05 | 12.05 | 12.05 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 -4535.7015 -4535.7015 37.315936 149.36468 4.0443367 -749.14966 -749.14966 0.037760434 -2247.5149 0.028145122 2.5665716 182.30831 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1352 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 | | 1.907e-06 | | |100.00 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6756 ave 6756 max 6756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53432 ave 53432 max 53432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106864 ave 106864 max 106864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106864 Ave neighs/atom = 79.0414 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.2026/numatoms.out 1352 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4535.70146751162-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4535.70146751162-1352*${isolated_atom_energy} variable adjusted_pe_metal equal -4535.70146751162-1352*0 print "${adjusted_pe_metal} eV" file output/dump_081.2026/energy.out -4535.70146751162 eV print "${mindist_metal} Angstroms" file output/dump_081.2026/mindistance.out 2.56657156819864 Angstroms write_dump all cfg output/dump_081.2026/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_081.2026/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:37