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 4.032082714140415*${_u_distance} variable lattice_constant_converted equal 4.032082714140415*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 67.10723068929734*${_u_distance} variable xmax_converted equal 67.10723068929734*1 variable ymin_converted equal -67.11126277201149*${_u_distance} variable ymin_converted equal -67.11126277201149*1 variable ymax_converted equal 67.11126277201149*${_u_distance} variable ymax_converted equal 67.11126277201149*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082714140415*${_u_distance} variable zmax_converted equal 4.032082714140415*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03208271414042 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 67.1072306892973 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.1072306892973 -67.1112627720115 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.1072306892973 -67.1112627720115 67.1112627720115 ${zmin_converted} ${zmax_converted} units box region whole block 0 67.1072306892973 -67.1112627720115 67.1112627720115 0 ${zmax_converted} units box region whole block 0 67.1072306892973 -67.1112627720115 67.1112627720115 0 4.03208271414042 units box create_box 2 whole Created orthogonal box = (0 -67.1113 0) to (67.1072 67.1113 4.03208) 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 67.1112627720115 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 lattice fcc 4.03208271414042 orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57208 5.57208 4.03208 create_atoms 1 region upper Created 1109 atoms create_atoms CPU = 0.000309944 secs group upper type 1 1109 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.489492639691956 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -67.1112627720115 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 lattice fcc 4.03208271414042 orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57208 5.57208 4.03208 create_atoms 2 region lower Created 1109 atoms create_atoms CPU = 0.000185013 secs group lower type 2 1109 atoms in group lower displace_atoms lower move -7.489492639691956 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_ErcolessiAdams_1994_Al__MO_324507536345_002 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*4.03208271414042 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604135707021 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 18 36 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2192 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 18 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.65 | 5.65 | 5.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7324.7639 0 -7324.7639 440.66727 267 0 -7347.9141 0 -7347.9141 -5133.2545 Loop time of 3.91453 on 1 procs for 267 steps with 2192 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 = -7324.76392812 -7347.91410331 -7347.91410331 Force two-norm initial, final = 24.6707 1.77322e-05 Force max component initial, final = 4.60626 5.3288e-06 Final line search alpha, max atom move = 1 5.3288e-06 Iterations, force evaluations = 267 527 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8488 | 3.8488 | 3.8488 | 0.0 | 98.32 Neigh | 0.005091 | 0.005091 | 0.005091 | 0.0 | 0.13 Comm | 0.036257 | 0.036257 | 0.036257 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02434 | | | 0.62 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12708 ave 12708 max 12708 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: 263248 ave 263248 max 263248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263248 Ave neighs/atom = 120.095 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) = 5.65 | 5.65 | 5.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 267 0 -7347.9141 0 -7347.9141 -5133.2545 36318.187 1267 0 -7348.179 0 -7348.179 -1147.6893 36136.115 Loop time of 15.8456 on 1 procs for 1000 steps with 2192 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 = -7347.91410331 -7348.17900349 -7348.17900356 Force two-norm initial, final = 146.823 0.04621 Force max component initial, final = 112.597 0.026623 Final line search alpha, max atom move = 0.0372913 0.000992804 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.231 | 15.231 | 15.231 | 0.0 | 96.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13096 | 0.13096 | 0.13096 | 0.0 | 0.83 Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4832 | | | 3.05 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12708 ave 12708 max 12708 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: 250710 ave 250710 max 250710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250710 Ave neighs/atom = 114.375 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 18 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.788 | 5.788 | 5.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7348.179 0 -7348.179 -1147.6893 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2192 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: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12718 ave 12718 max 12718 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: 264186 ave 264186 max 264186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264186 Ave neighs/atom = 120.523 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) = 5.788 | 5.788 | 5.788 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 -7348.179 -7348.179 66.904598 134.22253 4.0240196 -1147.6893 -1147.6893 -0.8252788 -3441.0645 -1.1780283 2.5091202 1083.0194 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2192 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: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12718 ave 12718 max 12718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132093 ave 132093 max 132093 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 264186 ave 264186 max 264186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264186 Ave neighs/atom = 120.523 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_065.4705/numatoms.out 2192 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7348.17900355761-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7348.17900355761-2192*${isolated_atom_energy} variable adjusted_pe_metal equal -7348.17900355761-2192*0 print "${adjusted_pe_metal} eV" file output/dump_065.4705/energy.out -7348.17900355761 eV print "${mindist_metal} Angstroms" file output/dump_065.4705/mindistance.out 2.50912015885885 Angstroms write_dump all cfg output/dump_065.4705/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_065.4705/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:19