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 3.9946166351437573*${_u_distance} variable lattice_constant_converted equal 3.9946166351437573*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 42.463357297553586*${_u_distance} variable xmax_converted equal 42.463357297553586*1 variable ymin_converted equal -42.46735191418873*${_u_distance} variable ymin_converted equal -42.46735191418873*1 variable ymax_converted equal 42.46735191418873*${_u_distance} variable ymax_converted equal 42.46735191418873*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.9946166351437573*${_u_distance} variable zmax_converted equal 3.9946166351437573*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.99461663514376 Lattice spacing in x,y,z = 3.99462 3.99462 3.99462 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 42.4633572975536 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.4633572975536 -42.4673519141887 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.4633572975536 -42.4673519141887 42.4673519141887 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.4633572975536 -42.4673519141887 42.4673519141887 0 ${zmax_converted} units box region whole block 0 42.4633572975536 -42.4673519141887 42.4673519141887 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -42.4674 0) to (42.4634 42.4674 3.99462) 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 42.4673519141887 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -7 0 orient y 7 8 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 8 -7 0 orient y 7 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.63673 5.63673 3.99462 create_atoms 1 region upper Created 454 atoms create_atoms CPU = 0.000250101 secs group upper type 1 454 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.783565615730593 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.4673519141887 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 7 0 orient y -7 8 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 8 7 0 orient y -7 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.63673 5.63673 3.99462 create_atoms 2 region lower Created 454 atoms create_atoms CPU = 0.00012207 secs group lower type 2 454 atoms in group lower displace_atoms lower move -4.783565615730593 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001 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*3.99461663514376 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.99730831757188 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 23 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 888 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2892.8509 0 -2892.8509 1047.6391 281 0 -2911.5469 0 -2911.5469 -6162.0372 Loop time of 3.1418 on 1 procs for 281 steps with 888 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2892.8508773 -2911.54692537 -2911.54692537 Force two-norm initial, final = 14.433 5.44881e-06 Force max component initial, final = 3.0846 7.93802e-07 Final line search alpha, max atom move = 1 7.93802e-07 Iterations, force evaluations = 281 529 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0997 | 3.0997 | 3.0997 | 0.0 | 98.66 Neigh | 0.011237 | 0.011237 | 0.011237 | 0.0 | 0.36 Comm | 0.019434 | 0.019434 | 0.019434 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01138 | | | 0.36 Nlocal: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6222 ave 6222 max 6222 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: 113744 ave 113744 max 113744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113744 Ave neighs/atom = 128.09 Neighbor list builds = 4 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) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 281 0 -2911.5469 0 -2911.5469 -6162.0372 14407.035 301 0 -2911.7495 0 -2911.7495 -2777.0452 14280.025 Loop time of 0.47759 on 1 procs for 20 steps with 888 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2911.54692537 -2911.74951665 -2911.74951665 Force two-norm initial, final = 46.685 0.152725 Force max component initial, final = 41.9946 0.128526 Final line search alpha, max atom move = 3.1835e-07 4.09163e-08 Iterations, force evaluations = 20 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46697 | 0.46697 | 0.46697 | 0.0 | 97.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002362 | 0.002362 | 0.002362 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008259 | | | 1.73 Nlocal: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6242 ave 6242 max 6242 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: 113952 ave 113952 max 113952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113952 Ave neighs/atom = 128.324 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 -6.30324000329931e-20 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2911.7495 0 -2911.7495 -2777.0452 Loop time of 9.53674e-07 on 1 procs for 0 steps with 888 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: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6242 ave 6242 max 6242 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: 114624 ave 114624 max 114624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114624 Ave neighs/atom = 129.081 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) = 5.092 | 5.092 | 5.092 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 -2911.7495 -2911.7495 42.522779 84.934704 3.9538678 -2777.0452 -2777.0452 -6.2497911 -8339.1588 14.273154 2.5640286 175.36347 Loop time of 9.53674e-07 on 1 procs for 0 steps with 888 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: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6242 ave 6242 max 6242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57312 ave 57312 max 57312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114624 ave 114624 max 114624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114624 Ave neighs/atom = 129.081 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_082.3719/numatoms.out 888 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2911.74951665482-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2911.74951665482-888*${isolated_atom_energy} variable adjusted_pe_metal equal -2911.74951665482-888*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_082.3719/energy.out -2911.74951665482 eV print "${mindist_metal} Angstroms" file output/dump_082.3719/mindistance.out 2.5640286325136 Angstroms write_dump all cfg output/dump_082.3719/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_082.3719/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03