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 4.031036108732224*${_u_distance} variable lattice_constant_converted equal 4.031036108732224*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 47.182067981985654*${_u_distance} variable xmax_converted equal 47.182067981985654*1 variable ymin_converted equal -47.18609901809439*${_u_distance} variable ymin_converted equal -47.18609901809439*1 variable ymax_converted equal 47.18609901809439*${_u_distance} variable ymax_converted equal 47.18609901809439*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031036108732224*${_u_distance} variable zmax_converted equal 4.031036108732224*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03103610873222 Lattice spacing in x,y,z = 4.03104 4.03104 4.03104 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 47.1820679819857 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.1820679819857 -47.1860990180944 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.1820679819857 -47.1860990180944 47.1860990180944 ${zmin_converted} ${zmax_converted} units box region whole block 0 47.1820679819857 -47.1860990180944 47.1860990180944 0 ${zmax_converted} units box region whole block 0 47.1820679819857 -47.1860990180944 47.1860990180944 0 4.03103610873222 units box create_box 2 whole Created orthogonal box = (0 -47.1861 0) to (47.1821 47.1861 4.03104) 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 47.1860990180944 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.16592 5.16592 4.03104 create_atoms 1 region upper Created 549 atoms create_atoms CPU = 0.000276089 secs group upper type 1 549 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.267114959823831 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -47.1860990180944 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.16592 5.16592 4.03104 create_atoms 2 region lower Created 549 atoms create_atoms CPU = 0.000146866 secs group lower type 2 549 atoms in group lower displace_atoms lower move -5.267114959823831 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005 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*4.03103610873222 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01551805436611 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 25 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1074 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3582.5706 0 -3582.5706 -1593.0668 237 0 -3594.3642 0 -3594.3642 -9385.0105 Loop time of 1.28149 on 1 procs for 237 steps with 1074 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3582.57064115 -3594.36421763 -3594.36421763 Force two-norm initial, final = 13.8439 5.80847e-06 Force max component initial, final = 4.34558 2.06599e-06 Final line search alpha, max atom move = 1 2.06599e-06 Iterations, force evaluations = 237 464 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2459 | 1.2459 | 1.2459 | 0.0 | 97.22 Neigh | 0.0070229 | 0.0070229 | 0.0070229 | 0.0 | 0.55 Comm | 0.017687 | 0.017687 | 0.017687 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01087 | | | 0.85 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7098 ave 7098 max 7098 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: 139700 ave 139700 max 139700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139700 Ave neighs/atom = 130.074 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) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press Volume 237 0 -3594.3642 0 -3594.3642 -9385.0105 17948.896 1237 0 -3594.7512 0 -3594.7512 -2752.7015 17783.465 Loop time of 5.57286 on 1 procs for 1000 steps with 1074 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3594.36421763 -3594.75124794 -3594.75124795 Force two-norm initial, final = 117.987 0.0095522 Force max component initial, final = 85.6525 0.00620048 Final line search alpha, max atom move = 0.132591 0.000822127 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.266 | 5.266 | 5.266 | 0.0 | 94.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.067988 | 0.067988 | 0.067988 | 0.0 | 1.22 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2388 | | | 4.29 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6818 ave 6818 max 6818 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: 139380 ave 139380 max 139380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139380 Ave neighs/atom = 129.777 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 13 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 5.143 | 5.143 | 5.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3594.7512 0 -3594.7512 -2752.7015 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6854 ave 6854 max 6854 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: 139928 ave 139928 max 139928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139928 Ave neighs/atom = 130.287 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) = 5.143 | 5.143 | 5.143 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 -3594.7512 -3594.7512 47.002804 94.372198 4.0091154 -2752.7015 -2752.7015 -0.23684426 -8257.3122 -0.55558581 2.5763254 864.46218 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6854 ave 6854 max 6854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69964 ave 69964 max 69964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139928 ave 139928 max 139928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139928 Ave neighs/atom = 130.287 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.9662/numatoms.out 1074 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3594.75124794967-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3594.75124794967-1074*${isolated_atom_energy} variable adjusted_pe_metal equal -3594.75124794967-1074*0 print "${adjusted_pe_metal} eV" file output/dump_039.9662/energy.out -3594.75124794967 eV print "${mindist_metal} Angstroms" file output/dump_039.9662/mindistance.out 2.57632540594372 Angstroms write_dump all cfg output/dump_039.9662/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_039.9662/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06