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 31.631502493702282*${_u_distance} variable xmax_converted equal 31.631502493702282*1 variable ymin_converted equal -63.26705498629145*${_u_distance} variable ymin_converted equal -63.26705498629145*1 variable ymax_converted equal 63.26705498629145*${_u_distance} variable ymax_converted equal 63.26705498629145*1 variable zmin_converted equal 0.0*${_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 31.6315024937023 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 31.6315024937023 -63.2670549862914 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 31.6315024937023 -63.2670549862914 63.2670549862914 ${zmin_converted} ${zmax_converted} units box region whole block 0 31.6315024937023 -63.2670549862914 63.2670549862914 0 ${zmax_converted} units box region whole block 0 31.6315024937023 -63.2670549862914 63.2670549862914 0 4.04999888688326 units box create_box 2 whole Created orthogonal box = (0 -63.2671 0) to (31.6315 63.2671 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 63.2670549862914 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 -5 0 orient y 5 6 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 6 -5 0 orient y 5 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70404 5.70404 4.05 create_atoms 1 region upper Created 490 atoms create_atoms CPU = 0.00026989 secs group upper type 1 490 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.514612354157994 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -63.2670549862914 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 5 0 orient y -5 6 0 orient z 0 0 1 lattice fcc 4.04999888688326 orient x 6 5 0 orient y -5 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70404 5.70404 4.05 create_atoms 2 region lower Created 490 atoms create_atoms CPU = 0.000105858 secs group lower type 2 490 atoms in group lower displace_atoms lower move -3.514612354157994 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 10 37 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 18 atoms, new total = 962 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 = 10 37 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) = 11.98 | 11.98 | 11.98 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3208.7165 0 -3208.7165 1942.588 442 0 -3221.8918 0 -3221.8918 -5832.2388 Loop time of 8.32588 on 1 procs for 442 steps with 962 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 = -3208.71650248 -3221.89182346 -3221.89182346 Force two-norm initial, final = 17.2739 1.13777e-05 Force max component initial, final = 4.9169 1.31258e-06 Final line search alpha, max atom move = 1 1.31258e-06 Iterations, force evaluations = 442 880 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2727 | 8.2727 | 8.2727 | 0.0 | 99.36 Neigh | 0.0020571 | 0.0020571 | 0.0020571 | 0.0 | 0.02 Comm | 0.030958 | 0.030958 | 0.030958 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02013 | | | 0.24 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5943 ave 5943 max 5943 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37662 ave 37662 max 37662 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75324 ave 75324 max 75324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75324 Ave neighs/atom = 78.2994 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) = 11.99 | 11.99 | 11.99 Mbytes Step Temp E_pair E_mol TotEng Press Volume 442 0 -3221.8918 0 -3221.8918 -5832.2388 16209.975 1442 0 -3222.1404 0 -3222.1404 -2692.876 16134.733 Loop time of 21.869 on 1 procs for 1000 steps with 962 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 = -3221.89182346 -3222.14037224 -3222.14037759 Force two-norm initial, final = 54.6103 0.193841 Force max component initial, final = 48.3128 0.143531 Final line search alpha, max atom move = 0.0056013 0.000803959 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.575 | 21.575 | 21.575 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.065341 | 0.065341 | 0.065341 | 0.0 | 0.30 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2281 | | | 1.04 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5970 ave 5970 max 5970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37802 ave 37802 max 37802 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75604 ave 75604 max 75604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75604 Ave neighs/atom = 78.5904 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 = 10 37 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) = 10.87 | 10.87 | 10.87 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3222.1404 0 -3222.1404 -2692.876 Loop time of 9.53674e-07 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5971 ave 5971 max 5971 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37982 ave 37982 max 37982 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75964 ave 75964 max 75964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75964 Ave neighs/atom = 78.9647 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) = 10.87 | 10.87 | 10.87 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 -3222.1404 -3222.1404 31.639892 126.53411 4.0301312 -2692.876 -2692.876 -12.140134 -8080.6704 14.182654 2.5732249 219.4137 Loop time of 9.53674e-07 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5971 ave 5971 max 5971 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37982 ave 37982 max 37982 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75964 ave 75964 max 75964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75964 Ave neighs/atom = 78.9647 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_079.6111/numatoms.out 962 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3222.14037759303-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3222.14037759303-962*${isolated_atom_energy} variable adjusted_pe_metal equal -3222.14037759303-962*0 print "${adjusted_pe_metal} eV" file output/dump_079.6111/energy.out -3222.14037759303 eV print "${mindist_metal} Angstroms" file output/dump_079.6111/mindistance.out 2.57322492098632 Angstroms write_dump all cfg output/dump_079.6111/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_079.6111/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:30