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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 16.698619918659933*${_u_distance} variable xmax_converted equal 16.698619918659933*1 variable ymin_converted equal -50.09990976619902*${_u_distance} variable ymin_converted equal -50.09990976619902*1 variable ymax_converted equal 50.09990976619902*${_u_distance} variable ymax_converted equal 50.09990976619902*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 16.6986199186599 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6986199186599 -50.099909766199 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6986199186599 -50.099909766199 50.099909766199 ${zmin_converted} ${zmax_converted} units box region whole block 0 16.6986199186599 -50.099909766199 50.099909766199 0 ${zmax_converted} units box region whole block 0 16.6986199186599 -50.099909766199 50.099909766199 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -50.0999 0) to (16.6986 50.0999 4.05001) 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 50.099909766199 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.91136 4.91136 4.05001 create_atoms 1 region upper Created 206 atoms create_atoms CPU = 0.000150919 secs group upper type 1 206 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.8553975315279474 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -50.099909766199 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.91136 4.91136 4.05001 create_atoms 2 region lower Created 206 atoms create_atoms CPU = 4.60148e-05 secs group lower type 2 206 atoms in group lower displace_atoms lower move -1.8553975315279474 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 5 27 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1355.9618 0 -1355.9618 4803.0349 209 0 -1364.7744 0 -1364.7744 -3051.1752 Loop time of 0.46778 on 1 procs for 209 steps with 404 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1355.96184613 -1364.77439031 -1364.77439031 Force two-norm initial, final = 21.0214 2.79737e-06 Force max component initial, final = 6.93579 6.1141e-07 Final line search alpha, max atom move = 1 6.1141e-07 Iterations, force evaluations = 209 414 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45243 | 0.45243 | 0.45243 | 0.0 | 96.72 Neigh | 0.001271 | 0.001271 | 0.001271 | 0.0 | 0.27 Comm | 0.0094478 | 0.0094478 | 0.0094478 | 0.0 | 2.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004628 | | | 0.99 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016 ave 4016 max 4016 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: 45004 ave 45004 max 45004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45004 Ave neighs/atom = 111.396 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) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 209 0 -1364.7744 0 -1364.7744 -3051.1752 6776.4718 1209 0 -1364.7988 0 -1364.7988 -221.76821 6750.8581 Loop time of 2.12225 on 1 procs for 1000 steps with 404 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 = -1364.77439031 -1364.79875382 -1364.79875391 Force two-norm initial, final = 18.0828 0.0165939 Force max component initial, final = 13.3527 0.0118478 Final line search alpha, max atom move = 0.0662477 0.000784892 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.953 | 1.953 | 1.953 | 0.0 | 92.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.040785 | 0.040785 | 0.040785 | 0.0 | 1.92 Output | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1284 | | | 6.05 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 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: 45040 ave 45040 max 45040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45040 Ave neighs/atom = 111.485 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1364.7988 0 -1364.7988 -221.76821 Loop time of 1.19209e-06 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 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: 47520 ave 47520 max 47520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47520 Ave neighs/atom = 117.624 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) = 4.601 | 4.601 | 4.601 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 -1364.7988 -1364.7988 16.658833 100.19982 4.0443382 -221.76821 -221.76821 2.8051381 -668.74124 0.6314644 2.6207486 238.75305 Loop time of 9.53674e-07 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23760 ave 23760 max 23760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47520 ave 47520 max 47520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47520 Ave neighs/atom = 117.624 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_028.0725/numatoms.out 404 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1364.798753914-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1364.798753914-404*${isolated_atom_energy} variable adjusted_pe_metal equal -1364.798753914-404*0 print "${adjusted_pe_metal} eV" file output/dump_028.0725/energy.out -1364.798753914 eV print "${mindist_metal} Angstroms" file output/dump_028.0725/mindistance.out 2.62074861702817 Angstroms write_dump all cfg output/dump_028.0725/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_028.0725/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02