LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 63.767147242860766*${_u_distance} variable xmax_converted equal 63.767147242860766*1 variable ymin_converted equal -63.77118023136434*${_u_distance} variable ymin_converted equal -63.77118023136434*1 variable ymax_converted equal 63.77118023136434*${_u_distance} variable ymax_converted equal 63.77118023136434*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 63.7671472428608 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.7671472428608 -63.7711802313643 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.7671472428608 -63.7711802313643 63.7711802313643 ${zmin_converted} ${zmax_converted} units box region whole block 0 63.7671472428608 -63.7711802313643 63.7711802313643 0 ${zmax_converted} units box region whole block 0 63.7671472428608 -63.7711802313643 63.7711802313643 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -63.7712 0) to (63.7671 63.7712 4.03299) 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 63.7711802313643 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -9 0 orient y 9 13 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 13 -9 0 orient y 9 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.61151 5.61151 4.03299 create_atoms 1 region upper Created 1002 atoms create_atoms CPU = 0.000300169 secs group upper type 1 1002 atoms in group upper mass 1 26.981538*${_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 -63.7711802313643 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 9 0 orient y -9 13 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 13 9 0 orient y -9 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.61151 5.61151 4.03299 create_atoms 2 region lower Created 1002 atoms create_atoms CPU = 0.000181913 secs group lower type 2 1002 atoms in group lower displace_atoms lower move -7.115124735378854 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 10 19 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 13.7567 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.96 | 13.96 | 13.96 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5701.7383 0 -5701.7383 1861.8784 348 0 -5762.3007 0 -5762.3007 -5433.8133 Loop time of 17.3283 on 1 procs for 348 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 = -5701.73827114 -5762.30069566 -5762.30069566 Force two-norm initial, final = 38.1054 7.21932e-05 Force max component initial, final = 7.38391 6.37078e-06 Final line search alpha, max atom move = 1 6.37078e-06 Iterations, force evaluations = 348 678 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.185 | 17.185 | 17.185 | 0.0 | 99.17 Neigh | 0.038033 | 0.038033 | 0.038033 | 0.0 | 0.22 Comm | 0.078967 | 0.078967 | 0.078967 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02609 | | | 0.15 Nlocal: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25556 ave 25556 max 25556 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: 1.31392e+06 ave 1.31392e+06 max 1.31392e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1313924 Ave neighs/atom = 663.598 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) = 13.96 | 13.96 | 13.96 Mbytes Step Temp E_pair E_mol TotEng Press Volume 348 0 -5762.3007 0 -5762.3007 -5433.8133 32800.346 1348 0 -5762.4486 0 -5762.4486 -2506.457 32669.004 Loop time of 52.6152 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 = -5762.30069566 -5762.44859559 -5762.44859617 Force two-norm initial, final = 102.656 0.125761 Force max component initial, final = 81.2368 0.106673 Final line search alpha, max atom move = 0.00846488 0.000902973 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 51.797 | 51.797 | 51.797 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.22505 | 0.22505 | 0.22505 | 0.0 | 0.43 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5934 | | | 1.13 Nlocal: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25572 ave 25572 max 25572 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: 1.30878e+06 ave 1.30878e+06 max 1.30878e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1308784 Ave neighs/atom = 661.002 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 13.47 | 13.47 | 13.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5762.4486 0 -5762.4486 -2506.457 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25604 ave 25604 max 25604 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: 1.31241e+06 ave 1.31241e+06 max 1.31241e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1312408 Ave neighs/atom = 662.832 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:52) Per MPI rank memory allocation (min/avg/max) = 13.47 | 13.47 | 13.47 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 -5762.4486 -5762.4486 63.628482 127.54236 4.0255932 -2506.457 -2506.457 -5.2201463 -7517.3637 3.2128262 2.5412791 644.87966 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 1980 ave 1980 max 1980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25604 ave 25604 max 25604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 656204 ave 656204 max 656204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.31241e+06 ave 1.31241e+06 max 1.31241e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1312408 Ave neighs/atom = 662.832 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -5762.4485961715-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5762.4485961715-1980*${isolated_atom_energy} variable adjusted_pe_metal equal -5762.4485961715-1980*0 print "${adjusted_pe_metal} eV" file output/dump_069.3903/energy.out -5762.4485961715 eV print "${mindist_metal} Angstroms" file output/dump_069.3903/mindistance.out 2.54127912675542 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: 0:01:10