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 4.032073378562927*${_u_distance} variable lattice_constant_converted equal 4.032073378562927*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 48.55259293659608*${_u_distance} variable xmax_converted equal 48.55259293659608*1 variable ymin_converted equal -48.55662500997464*${_u_distance} variable ymin_converted equal -48.55662500997464*1 variable ymax_converted equal 48.55662500997464*${_u_distance} variable ymax_converted equal 48.55662500997464*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032073378562927*${_u_distance} variable zmax_converted equal 4.032073378562927*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03207337856293 Lattice spacing in x,y,z = 4.03207 4.03207 4.03207 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 48.5525929365961 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.5525929365961 -48.5566250099746 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.5525929365961 -48.5566250099746 48.5566250099746 ${zmin_converted} ${zmax_converted} units box region whole block 0 48.5525929365961 -48.5566250099746 48.5566250099746 0 ${zmax_converted} units box region whole block 0 48.5525929365961 -48.5566250099746 48.5566250099746 0 4.03207337856293 units box create_box 2 whole Created orthogonal box = (0 -48.5566 0) to (48.5526 48.5566 4.03207) 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 48.5566250099746 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -8 0 orient y 8 9 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 9 -8 0 orient y 8 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69237 5.69237 4.03207 create_atoms 1 region upper Created 582 atoms create_atoms CPU = 0.000311136 secs group upper type 1 582 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.418717560456534 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -48.5566250099746 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 8 0 orient y -8 9 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 9 8 0 orient y -8 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69237 5.69237 4.03207 create_atoms 2 region lower Created 582 atoms create_atoms CPU = 0.000174046 secs group lower type 2 582 atoms in group lower displace_atoms lower move -5.418717560456534 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_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*4.03207337856293 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01603668928146 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 26 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1144 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.023 | 5.023 | 5.023 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3811.7961 0 -3811.7961 1714.4277 216 0 -3834.8806 0 -3834.8806 -7725.6048 Loop time of 1.16468 on 1 procs for 216 steps with 1144 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 = -3811.79613234 -3834.88060075 -3834.88060075 Force two-norm initial, final = 25.3741 3.19494e-06 Force max component initial, final = 5.30448 7.7116e-07 Final line search alpha, max atom move = 1 7.7116e-07 Iterations, force evaluations = 216 424 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1339 | 1.1339 | 1.1339 | 0.0 | 97.36 Neigh | 0.0038981 | 0.0038981 | 0.0038981 | 0.0 | 0.33 Comm | 0.016774 | 0.016774 | 0.016774 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01009 | | | 0.87 Nlocal: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566 ave 7566 max 7566 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: 148784 ave 148784 max 148784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148784 Ave neighs/atom = 130.056 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) = 5.023 | 5.023 | 5.023 Mbytes Step Temp E_pair E_mol TotEng Press Volume 216 0 -3834.8806 0 -3834.8806 -7725.6048 19011.63 1216 0 -3835.1551 0 -3835.1551 -2141.4243 18877.036 Loop time of 5.7845 on 1 procs for 1000 steps with 1144 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 = -3834.88060075 -3835.15506249 -3835.1550625 Force two-norm initial, final = 107.992 0.00802479 Force max component initial, final = 81.8646 0.00440167 Final line search alpha, max atom move = 0.139361 0.000613419 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4528 | 5.4528 | 5.4528 | 0.0 | 94.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.073952 | 0.073952 | 0.073952 | 0.0 | 1.28 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2577 | | | 4.46 Nlocal: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566 ave 7566 max 7566 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: 149536 ave 149536 max 149536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149536 Ave neighs/atom = 130.713 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 5.161 | 5.161 | 5.161 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3835.1551 0 -3835.1551 -2141.4243 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1144 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 | | 2.146e-06 | | |100.00 Nlocal: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566 ave 7566 max 7566 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: 149972 ave 149972 max 149972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149972 Ave neighs/atom = 131.094 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) = 5.161 | 5.161 | 5.161 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 -3835.1551 -3835.1551 48.356127 97.11325 4.0197941 -2141.4243 -2141.4243 0.37207699 -6424.778 0.13286074 2.532689 415.4236 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1144 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: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566 ave 7566 max 7566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74986 ave 74986 max 74986 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149972 ave 149972 max 149972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149972 Ave neighs/atom = 131.094 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_083.2671/numatoms.out 1144 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3835.15506250083-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3835.15506250083-1144*${isolated_atom_energy} variable adjusted_pe_metal equal -3835.15506250083-1144*0 print "${adjusted_pe_metal} eV" file output/dump_083.2671/energy.out -3835.15506250083 eV print "${mindist_metal} Angstroms" file output/dump_083.2671/mindistance.out 2.53268903320342 Angstroms write_dump all cfg output/dump_083.2671/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_083.2671/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:07