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 12.632086946252084*${_u_distance} variable xmax_converted equal 12.632086946252084*1 variable ymin_converted equal -50.53234240164348*${_u_distance} variable ymin_converted equal -50.53234240164348*1 variable ymax_converted equal 50.53234240164348*${_u_distance} variable ymax_converted equal 50.53234240164348*1 variable zmin_converted equal 0.0*${_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 12.6320869462521 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.6320869462521 -50.5323424016435 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.6320869462521 -50.5323424016435 50.5323424016435 ${zmin_converted} ${zmax_converted} units box region whole block 0 12.6320869462521 -50.5323424016435 50.5323424016435 0 ${zmax_converted} units box region whole block 0 12.6320869462521 -50.5323424016435 50.5323424016435 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -50.5323 0) to (12.6321 50.5323 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 50.5323424016435 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.05283 5.05283 3.99462 create_atoms 1 region upper Created 162 atoms create_atoms CPU = 0.000192165 secs group upper type 1 162 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -50.5323424016435 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.05283 5.05283 3.99462 create_atoms 2 region lower Created 162 atoms create_atoms CPU = 6.79493e-05 secs group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 4 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 318 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 = 4 27 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) = 4.45 | 4.45 | 4.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1032.3651 0 -1032.3651 5739.6696 84 0 -1041.2731 0 -1041.2731 -172.17083 Loop time of 0.459854 on 1 procs for 84 steps with 318 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -1032.36506757 -1041.27306225 -1041.27306225 Force two-norm initial, final = 16.707 0.00522948 Force max component initial, final = 4.23164 0.000908899 Final line search alpha, max atom move = 0.000244141 2.21899e-07 Iterations, force evaluations = 84 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45292 | 0.45292 | 0.45292 | 0.0 | 98.49 Neigh | 0.001101 | 0.001101 | 0.001101 | 0.0 | 0.24 Comm | 0.0040095 | 0.0040095 | 0.0040095 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001822 | | | 0.40 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3683 ave 3683 max 3683 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: 41552 ave 41552 max 41552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41552 Ave neighs/atom = 130.667 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) = 4.45 | 4.45 | 4.45 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -1041.2731 0 -1041.2731 -172.17083 5099.7588 104 0 -1041.2773 0 -1041.2773 347.6016 5093.1189 Loop time of 0.165774 on 1 procs for 20 steps with 318 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -1041.27306225 -1041.27725159 -1041.27725159 Force two-norm initial, final = 3.65753 0.0264806 Force max component initial, final = 3.59483 0.0193875 Final line search alpha, max atom move = 1.44645e-05 2.80429e-07 Iterations, force evaluations = 20 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16069 | 0.16069 | 0.16069 | 0.0 | 96.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012498 | 0.0012498 | 0.0012498 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003837 | | | 2.31 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3564 ave 3564 max 3564 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: 41768 ave 41768 max 41768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41768 Ave neighs/atom = 131.346 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 = 4 27 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1041.2773 0 -1041.2773 347.6016 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3560 ave 3560 max 3560 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: 41780 ave 41780 max 41780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41780 Ave neighs/atom = 131.384 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) = 4.587 | 4.587 | 4.587 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 -1041.2773 -1041.2773 12.599764 101.06468 3.9996499 347.6016 347.6016 6.0832366 1041.2245 -4.502948 2.5456791 213.9719 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3560 ave 3560 max 3560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20890 ave 20890 max 20890 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41780 ave 41780 max 41780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41780 Ave neighs/atom = 131.384 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1041.27725158723-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1041.27725158723-318*${isolated_atom_energy} variable adjusted_pe_metal equal -1041.27725158723-318*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_036.8699/energy.out -1041.27725158723 eV print "${mindist_metal} Angstroms" file output/dump_036.8699/mindistance.out 2.54567912704334 Angstroms write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00