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 74.49489294495585*${_u_distance} variable xmax_converted equal 74.49489294495585*1 variable ymin_converted equal -74.49910364525917*${_u_distance} variable ymin_converted equal -74.49910364525917*1 variable ymax_converted equal 74.49910364525917*${_u_distance} variable ymax_converted equal 74.49910364525917*1 variable zmin_converted equal 0.0*${_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 74.4948929449559 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 74.4948929449559 -74.4991036452592 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 74.4948929449559 -74.4991036452592 74.4991036452592 ${zmin_converted} ${zmax_converted} units box region whole block 0 74.4948929449559 -74.4991036452592 74.4991036452592 0 ${zmax_converted} units box region whole block 0 74.4948929449559 -74.4991036452592 74.4991036452592 0 4.21070030331612 units box create_box 2 whole Created orthogonal box = (0 -74.4991 0) to (74.4949 74.4991 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 74.4991036452592 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -12 0 orient y 12 13 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 13 -12 0 orient y 12 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.95007 5.95007 4.2107 create_atoms 1 region upper Created 1254 atoms create_atoms CPU = 0.000329018 secs group upper type 1 1254 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.96131270582936 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.4991036452592 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 12 0 orient y -12 13 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 13 12 0 orient y -12 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.95007 5.95007 4.2107 create_atoms 2 region lower Created 1254 atoms create_atoms CPU = 0.000211954 secs group lower type 2 1254 atoms in group lower displace_atoms lower move -7.96131270582936 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 17 34 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 32 atoms, new total = 2476 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 = 17 34 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) = 10.41 | 10.41 | 10.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9201.9915 0 -9201.9915 -38.307374 496 0 -9221.5726 0 -9221.5726 -3071.5637 Loop time of 15.7531 on 1 procs for 496 steps with 2476 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 = -9201.99149684 -9221.57258191 -9221.57258191 Force two-norm initial, final = 20.3458 3.13979e-05 Force max component initial, final = 3.6015 3.57809e-06 Final line search alpha, max atom move = 1 3.57809e-06 Iterations, force evaluations = 496 978 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.59 | 15.59 | 15.59 | 0.0 | 98.97 Neigh | 0.020458 | 0.020458 | 0.020458 | 0.0 | 0.13 Comm | 0.089435 | 0.089435 | 0.089435 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05277 | | | 0.33 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14815 ave 14815 max 14815 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: 417592 ave 417592 max 417592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417592 Ave neighs/atom = 168.656 Neighbor list builds = 2 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) = 10.41 | 10.41 | 10.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 496 0 -9221.5726 0 -9221.5726 -3071.5637 46737.112 1496 0 -9221.8286 0 -9221.8286 -599.59833 46433.774 Loop time of 32.5624 on 1 procs for 1000 steps with 2476 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 = -9221.57258191 -9221.82856911 -9221.82857042 Force two-norm initial, final = 109.986 0.189905 Force max component initial, final = 80.4394 0.143773 Final line search alpha, max atom move = 0.0186743 0.00268487 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.84 | 31.84 | 31.84 | 0.0 | 97.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1589 | 0.1589 | 0.1589 | 0.0 | 0.49 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5637 | | | 1.73 Nlocal: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14726 ave 14726 max 14726 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: 417644 ave 417644 max 417644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417644 Ave neighs/atom = 168.677 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 = 17 34 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) = 9.922 | 9.922 | 9.922 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9221.8286 0 -9221.8286 -599.59833 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2476 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: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14736 ave 14736 max 14736 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: 422216 ave 422216 max 422216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422216 Ave neighs/atom = 170.523 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) = 9.922 | 9.922 | 9.922 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 -9221.8286 -9221.8286 74.202299 148.99821 4.1998674 -599.59833 -599.59833 -4.1612913 -1789.6856 -4.9480737 2.7392045 892.02027 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2476 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: 2476 ave 2476 max 2476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14736 ave 14736 max 14736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211108 ave 211108 max 211108 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 422216 ave 422216 max 422216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422216 Ave neighs/atom = 170.523 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.4188/numatoms.out 2476 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9221.82857042116-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9221.82857042116-2476*${isolated_atom_energy} variable adjusted_pe_metal equal -9221.82857042116-2476*0 print "${adjusted_pe_metal} eV" file output/dump_085.4188/energy.out -9221.82857042116 eV print "${mindist_metal} Angstroms" file output/dump_085.4188/mindistance.out 2.73920445894423 Angstroms write_dump all cfg output/dump_085.4188/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_085.4188/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:48