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 4.031999975442886*${_u_distance} variable lattice_constant_converted equal 4.031999975442886*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 67.1058536429281*${_u_distance} variable xmax_converted equal 67.1058536429281*1 variable ymin_converted equal -67.10988564290354*${_u_distance} variable ymin_converted equal -67.10988564290354*1 variable ymax_converted equal 67.10988564290354*${_u_distance} variable ymax_converted equal 67.10988564290354*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031999975442886*${_u_distance} variable zmax_converted equal 4.031999975442886*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03199997544289 Lattice spacing in x,y,z = 4.032 4.032 4.032 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 67.1058536429281 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.1058536429281 -67.1098856429035 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 67.1058536429281 -67.1098856429035 67.1098856429035 ${zmin_converted} ${zmax_converted} units box region whole block 0 67.1058536429281 -67.1098856429035 67.1098856429035 0 ${zmax_converted} units box region whole block 0 67.1058536429281 -67.1098856429035 67.1098856429035 0 4.03199997544289 units box create_box 2 whole Created orthogonal box = (0 -67.1099 0) to (67.1059 67.1099 4.032) 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 67.1098856429035 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 14 -9 0 orient y 9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57197 5.57197 4.032 create_atoms 1 region upper Created 1110 atoms create_atoms CPU = 0.00030899 secs group upper type 1 1110 atoms in group upper mass 1 26.981538*${_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 -67.1098856429035 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 lattice fcc 4.03199997544289 orient x 14 9 0 orient y -9 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57197 5.57197 4.032 create_atoms 2 region lower Created 1110 atoms create_atoms CPU = 0.000201941 secs group lower type 2 1110 atoms in group lower displace_atoms lower move -7.489492639691956 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000 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*4.03199997544289 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01599998772144 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 16 31 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 16 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.956 | 9.956 | 9.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7328.5611 0 -7328.5611 -711.12988 302 0 -7347.5397 0 -7347.5397 -4963.3561 Loop time of 4.96875 on 1 procs for 302 steps with 2192 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7328.56114308 -7347.53965278 -7347.53965278 Force two-norm initial, final = 19.6074 4.17758e-06 Force max component initial, final = 3.50936 7.79526e-07 Final line search alpha, max atom move = 1 7.79526e-07 Iterations, force evaluations = 302 596 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8861 | 4.8861 | 4.8861 | 0.0 | 98.34 Neigh | 0.006218 | 0.006218 | 0.006218 | 0.0 | 0.13 Comm | 0.048944 | 0.048944 | 0.048944 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02752 | | | 0.55 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14611 ave 14611 max 14611 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: 384012 ave 384012 max 384012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384012 Ave neighs/atom = 175.188 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) = 9.956 | 9.956 | 9.956 Mbytes Step Temp E_pair E_mol TotEng Press Volume 302 0 -7347.5397 0 -7347.5397 -4963.3561 36315.951 1302 0 -7347.7655 0 -7347.7655 -1208.5659 36144.577 Loop time of 17.9118 on 1 procs for 1000 steps with 2192 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -7347.53965278 -7347.76546717 -7347.76546717 Force two-norm initial, final = 133.741 0.00314864 Force max component initial, final = 96.877 0.00159801 Final line search alpha, max atom move = 0.287599 0.000459586 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.282 | 17.282 | 17.282 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13789 | 0.13789 | 0.13789 | 0.0 | 0.77 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4919 | | | 2.75 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13478 ave 13478 max 13478 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: 383836 ave 383836 max 383836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383836 Ave neighs/atom = 175.108 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 16 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 9.457 | 9.457 | 9.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7347.7655 0 -7347.7655 -1208.5659 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13478 ave 13478 max 13478 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: 384048 ave 384048 max 384048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384048 Ave neighs/atom = 175.204 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) = 9.457 | 9.457 | 9.457 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 -7347.7655 -7347.7655 66.998825 134.21977 4.0193837 -1208.5659 -1208.5659 -0.070721752 -3625.5569 -0.069940108 2.5087036 1080.7733 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 2192 ave 2192 max 2192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13478 ave 13478 max 13478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 192024 ave 192024 max 192024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 384048 ave 384048 max 384048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384048 Ave neighs/atom = 175.204 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -7347.76546716659-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7347.76546716659-2192*${isolated_atom_energy} variable adjusted_pe_metal equal -7347.76546716659-2192*0 print "${adjusted_pe_metal} eV" file output/dump_065.4705/energy.out -7347.76546716659 eV print "${mindist_metal} Angstroms" file output/dump_065.4705/mindistance.out 2.50870357949665 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: 0:00:23