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 4.210700303316116*${_u_distance} variable lattice_constant_converted equal 4.210700303316116*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 60.28805349396363*${_u_distance} variable xmax_converted equal 60.28805349396363*1 variable ymin_converted equal -60.29226419426695*${_u_distance} variable ymin_converted equal -60.29226419426695*1 variable ymax_converted equal 60.29226419426695*${_u_distance} variable ymax_converted equal 60.29226419426695*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210700303316116*${_u_distance} variable zmax_converted equal 4.210700303316116*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21070030331612 Lattice spacing in x,y,z = 4.2107 4.2107 4.2107 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 60.2880534939636 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2880534939636 -60.2922641942669 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2880534939636 -60.2922641942669 60.2922641942669 ${zmin_converted} ${zmax_converted} units box region whole block 0 60.2880534939636 -60.2922641942669 60.2922641942669 0 ${zmax_converted} units box region whole block 0 60.2880534939636 -60.2922641942669 60.2922641942669 0 4.21070030331612 units box create_box 2 whole Created orthogonal box = (0 -60.2923 0) to (60.2881 60.2923 4.2107) 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 60.2922641942669 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -3 0 orient y 3 14 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 14 -3 0 orient y 3 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9995 4.9995 4.2107 create_atoms 1 region upper Created 822 atoms create_atoms CPU = 0.00032711 secs group upper type 1 822 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.44301947847436 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -60.2922641942669 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 3 0 orient y -3 14 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 14 3 0 orient y -3 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9995 4.9995 4.2107 create_atoms 2 region lower Created 822 atoms create_atoms CPU = 0.000181913 secs group lower type 2 822 atoms in group lower displace_atoms lower move -6.44301947847436 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.21070030331612 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535015165806 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 14 27 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1620 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 14 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6017.6038 0 -6017.6038 338.01918 498 0 -6030.6236 0 -6030.6236 -2230.7468 Loop time of 10.8726 on 1 procs for 498 steps with 1620 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 = -6017.60376038 -6030.62362459 -6030.62362459 Force two-norm initial, final = 17.7797 2.14769e-05 Force max component initial, final = 4.16747 1.86214e-06 Final line search alpha, max atom move = 1 1.86214e-06 Iterations, force evaluations = 498 986 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.768 | 10.768 | 10.768 | 0.0 | 99.03 Neigh | 0.0067339 | 0.0067339 | 0.0067339 | 0.0 | 0.06 Comm | 0.061824 | 0.061824 | 0.061824 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03646 | | | 0.34 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10493 ave 10493 max 10493 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: 277552 ave 277552 max 277552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 277552 Ave neighs/atom = 171.328 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) = 5.562 | 5.562 | 5.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 498 0 -6030.6236 0 -6030.6236 -2230.7468 30610.976 1498 0 -6030.6977 0 -6030.6977 -586.92446 30480.711 Loop time of 20.29 on 1 procs for 1000 steps with 1620 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 = -6030.62362459 -6030.69771491 -6030.6977151 Force two-norm initial, final = 49.0913 0.0360157 Force max component initial, final = 35.0322 0.0301473 Final line search alpha, max atom move = 0.162108 0.00488713 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.785 | 19.785 | 19.785 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11537 | 0.11537 | 0.11537 | 0.0 | 0.57 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3896 | | | 1.92 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11222 ave 11222 max 11222 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: 278212 ave 278212 max 278212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278212 Ave neighs/atom = 171.736 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 14 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.702 | 5.702 | 5.702 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6030.6977 0 -6030.6977 -586.92446 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11431 ave 11431 max 11431 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: 278864 ave 278864 max 278864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278864 Ave neighs/atom = 172.138 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) = 5.702 | 5.702 | 5.702 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 -6030.6977 -6030.6977 60.153027 120.58453 4.2021932 -586.92446 -586.92446 -1.5811023 -1758.801 -0.39128563 2.7312551 1101.3722 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11431 ave 11431 max 11431 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 139432 ave 139432 max 139432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 278864 ave 278864 max 278864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278864 Ave neighs/atom = 172.138 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_024.1895/numatoms.out 1620 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6030.69771510381-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6030.69771510381-1620*${isolated_atom_energy} variable adjusted_pe_metal equal -6030.69771510381-1620*0 print "${adjusted_pe_metal} eV" file output/dump_024.1895/energy.out -6030.69771510381 eV print "${mindist_metal} Angstroms" file output/dump_024.1895/mindistance.out 2.73125508090932 Angstroms write_dump all cfg output/dump_024.1895/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_024.1895/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:31