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 4.040926471352577*${_u_distance} variable lattice_constant_converted equal 4.040926471352577*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 25.87455423040168*${_u_distance} variable xmax_converted equal 25.87455423040168*1 variable ymin_converted equal -51.75314938727472*${_u_distance} variable ymin_converted equal -51.75314938727472*1 variable ymax_converted equal 51.75314938727472*${_u_distance} variable ymax_converted equal 51.75314938727472*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.040926471352577*${_u_distance} variable zmax_converted equal 4.040926471352577*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04092647135258 Lattice spacing in x,y,z = 4.04093 4.04093 4.04093 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 25.8745542304017 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.8745542304017 -51.7531493872747 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.8745542304017 -51.7531493872747 51.7531493872747 ${zmin_converted} ${zmax_converted} units box region whole block 0 25.8745542304017 -51.7531493872747 51.7531493872747 0 ${zmax_converted} units box region whole block 0 25.8745542304017 -51.7531493872747 51.7531493872747 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -51.7531 0) to (25.8746 51.7531 4.04093) 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 51.7531493872747 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67978 5.67978 4.04093 create_atoms 1 region upper Created 330 atoms create_atoms CPU = 0.00022316 secs group upper type 1 330 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.881405906844782 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.7531493872747 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67978 5.67978 4.04093 create_atoms 2 region lower Created 330 atoms create_atoms CPU = 7.60555e-05 secs group lower type 2 330 atoms in group lower displace_atoms lower move -2.881405906844782 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000 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*4.04092647135258 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02046323567629 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 21 1 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 648 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2514.1013 0 -2514.1013 1081.6209 319 0 -2524.2384 0 -2524.2384 -4725.8204 Loop time of 2.88894 on 1 procs for 319 steps with 648 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 = -2514.10127158 -2524.23839399 -2524.23839399 Force two-norm initial, final = 16.1733 2.59377e-07 Force max component initial, final = 4.52528 6.98773e-08 Final line search alpha, max atom move = 1 6.98773e-08 Iterations, force evaluations = 319 631 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8483 | 2.8483 | 2.8483 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02855 | 0.02855 | 0.02855 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01208 | | | 0.42 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7524 ave 7524 max 7524 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: 159136 ave 159136 max 159136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159136 Ave neighs/atom = 245.58 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) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 319 0 -2524.2384 0 -2524.2384 -4725.8204 10822.326 1319 0 -2524.3041 0 -2524.3041 -1027.9519 10773.296 Loop time of 9.10334 on 1 procs for 1000 steps with 648 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 = -2524.23839399 -2524.3041261 -2524.30412611 Force two-norm initial, final = 40.4104 0.00421701 Force max component initial, final = 29.8451 0.00316282 Final line search alpha, max atom move = 0.510426 0.00161439 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7784 | 8.7784 | 8.7784 | 0.0 | 96.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.082619 | 0.082619 | 0.082619 | 0.0 | 0.91 Output | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2423 | | | 2.66 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7548 ave 7548 max 7548 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: 158932 ave 158932 max 158932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158932 Ave neighs/atom = 245.265 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2524.3041 0 -2524.3041 -1027.9519 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 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: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7560 ave 7560 max 7560 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: 159096 ave 159096 max 159096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159096 Ave neighs/atom = 245.519 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) = 5.097 | 5.097 | 5.097 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 -2524.3041 -2524.3041 25.830748 103.5063 4.0294414 -1027.9519 -1027.9519 -0.46957036 -3083.264 -0.12206602 2.5022716 275.72082 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 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: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7560 ave 7560 max 7560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79548 ave 79548 max 79548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159096 ave 159096 max 159096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159096 Ave neighs/atom = 245.519 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_077.3196/numatoms.out 648 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2524.30412610646-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2524.30412610646-648*${isolated_atom_energy} variable adjusted_pe_metal equal -2524.30412610646-648*0 print "${adjusted_pe_metal} eV" file output/dump_077.3196/energy.out -2524.30412610646 eV print "${mindist_metal} Angstroms" file output/dump_077.3196/mindistance.out 2.50227163147368 Angstroms write_dump all cfg output/dump_077.3196/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_077.3196/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12