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 4.040926471352577*${_u_distance} variable lattice_constant_converted equal 4.040926471352577*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 63.892657533706476*${_u_distance} variable xmax_converted equal 63.892657533706476*1 variable ymin_converted equal -63.89669846017783*${_u_distance} variable ymin_converted equal -63.89669846017783*1 variable ymax_converted equal 63.89669846017783*${_u_distance} variable ymax_converted equal 63.89669846017783*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.040926471352577*${_u_distance} variable zmax_converted equal 4.040926471352577*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04092647135258 Lattice spacing in x,y,z = 4.04093 4.04093 4.04093 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 63.8926575337065 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.8926575337065 -63.8966984601778 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.8926575337065 -63.8966984601778 63.8966984601778 ${zmin_converted} ${zmax_converted} units box region whole block 0 63.8926575337065 -63.8966984601778 63.8966984601778 0 ${zmax_converted} units box region whole block 0 63.8926575337065 -63.8966984601778 63.8966984601778 0 4.04092647135258 units box create_box 2 whole Created orthogonal box = (0 -63.8967 0) to (63.8927 63.8967 4.04093) 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 63.8966984601778 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -9 0 orient y 9 13 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 13 -9 0 orient y 9 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.62255 5.62255 4.04093 create_atoms 1 region upper Created 1002 atoms create_atoms CPU = 0.000298977 secs group upper type 1 1002 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.115124735378854 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -63.8966984601778 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 9 0 orient y -9 13 0 orient z 0 0 1 lattice fcc 4.04092647135258 orient x 13 9 0 orient y -9 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.62255 5.62255 4.04093 create_atoms 2 region lower Created 1002 atoms create_atoms CPU = 0.000173092 secs group lower type 2 1002 atoms in group lower displace_atoms lower move -7.115124735378854 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_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*4.04092647135258 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02046323567629 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 13 26 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1980 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 13 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7687.7352 0 -7687.7352 1390.3448 268 0 -7715.7153 0 -7715.7153 -3615.1564 Loop time of 6.79264 on 1 procs for 268 steps with 1980 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 = -7687.73519065 -7715.71533386 -7715.71533386 Force two-norm initial, final = 28.1002 2.04927e-05 Force max component initial, final = 6.17715 5.3602e-06 Final line search alpha, max atom move = 1 5.3602e-06 Iterations, force evaluations = 268 529 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.72 | 6.72 | 6.72 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.049438 | 0.049438 | 0.049438 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02315 | | | 0.34 Nlocal: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16032 ave 16032 max 16032 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: 487024 ave 487024 max 487024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487024 Ave neighs/atom = 245.972 Neighbor list builds = 0 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) = 10.33 | 10.33 | 10.33 Mbytes Step Temp E_pair E_mol TotEng Press Volume 268 0 -7715.7153 0 -7715.7153 -3615.1564 32994.406 1268 0 -7715.8455 0 -7715.8455 -622.02429 32873.479 Loop time of 27.6689 on 1 procs for 1000 steps with 1980 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 = -7715.71533386 -7715.84554684 -7715.84554688 Force two-norm initial, final = 99.485 0.0216927 Force max component initial, final = 72.7463 0.0161366 Final line search alpha, max atom move = 0.0899677 0.00145177 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.934 | 26.934 | 26.934 | 0.0 | 97.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17472 | 0.17472 | 0.17472 | 0.0 | 0.63 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.56 | | | 2.02 Nlocal: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16014 ave 16014 max 16014 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: 487388 ave 487388 max 487388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487388 Ave neighs/atom = 246.156 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 13 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 9.841 | 9.841 | 9.841 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7715.8455 0 -7715.8455 -622.02429 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1980 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: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16032 ave 16032 max 16032 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: 487692 ave 487692 max 487692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487692 Ave neighs/atom = 246.309 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) = 9.841 | 9.841 | 9.841 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 -7715.8455 -7715.8455 63.799541 127.7934 4.0319923 -622.02429 -622.02429 0.78531402 -1866.9411 0.082884197 2.4914398 878.99634 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1980 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: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16032 ave 16032 max 16032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243846 ave 243846 max 243846 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 487692 ave 487692 max 487692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 487692 Ave neighs/atom = 246.309 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_069.3903/numatoms.out 1980 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7715.84554687902-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7715.84554687902-1980*${isolated_atom_energy} variable adjusted_pe_metal equal -7715.84554687902-1980*0 print "${adjusted_pe_metal} eV" file output/dump_069.3903/energy.out -7715.84554687902 eV print "${mindist_metal} Angstroms" file output/dump_069.3903/mindistance.out 2.49143982076503 Angstroms write_dump all cfg output/dump_069.3903/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_069.3903/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:34