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 34.69307890599845*${_u_distance} variable xmax_converted equal 34.69307890599845*1 variable ymin_converted equal -69.39019080050048*${_u_distance} variable ymin_converted equal -69.39019080050048*1 variable ymax_converted equal 69.39019080050048*${_u_distance} variable ymax_converted equal 69.39019080050048*1 variable zmin_converted equal 0.0*${_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 34.6930789059984 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.6930789059984 -69.3901908005005 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.6930789059984 -69.3901908005005 69.3901908005005 ${zmin_converted} ${zmax_converted} units box region whole block 0 34.6930789059984 -69.3901908005005 69.3901908005005 0 ${zmax_converted} units box region whole block 0 34.6930789059984 -69.3901908005005 69.3901908005005 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -69.3902 0) to (34.6931 69.3902 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 69.3901908005005 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -5 0 orient y 5 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 -5 0 orient y 5 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.6259 5.6259 4.03299 create_atoms 1 region upper Created 593 atoms create_atoms CPU = 0.000231981 secs group upper type 1 593 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.871046370169182 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -69.3901908005005 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 5 0 orient y -5 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 5 0 orient y -5 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.6259 5.6259 4.03299 create_atoms 2 region lower Created 593 atoms create_atoms CPU = 0.000129938 secs group lower type 2 593 atoms in group lower displace_atoms lower move -3.871046370169182 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 6 21 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 16 atoms, new total = 1170 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 = 6 21 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) = 11.44 | 11.44 | 11.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3371.9062 0 -3371.9062 605.25985 573 0 -3405.8377 0 -3405.8377 -6970.4097 Loop time of 17.1896 on 1 procs for 573 steps with 1170 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 = -3371.90620934 -3405.83772435 -3405.83772435 Force two-norm initial, final = 21.2817 2.01439e-05 Force max component initial, final = 6.36482 2.87579e-06 Final line search alpha, max atom move = 1 2.87579e-06 Iterations, force evaluations = 573 1115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.024 | 17.024 | 17.024 | 0.0 | 99.04 Neigh | 0.043595 | 0.043595 | 0.043595 | 0.0 | 0.25 Comm | 0.094739 | 0.094739 | 0.094739 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02724 | | | 0.16 Nlocal: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18736 ave 18736 max 18736 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: 772852 ave 772852 max 772852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 772852 Ave neighs/atom = 660.557 Neighbor list builds = 4 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) = 11.44 | 11.44 | 11.44 Mbytes Step Temp E_pair E_mol TotEng Press Volume 573 0 -3405.8377 0 -3405.8377 -6970.4097 19417.705 1573 0 -3405.9849 0 -3405.9849 -3012.0312 19313.05 Loop time of 31.6681 on 1 procs for 1000 steps with 1170 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 = -3405.83772435 -3405.98491269 -3405.98491272 Force two-norm initial, final = 75.2905 0.0318622 Force max component initial, final = 55.06 0.0255025 Final line search alpha, max atom move = 0.211155 0.00538499 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.093 | 31.093 | 31.093 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.16225 | 0.16225 | 0.16225 | 0.0 | 0.51 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4129 | | | 1.30 Nlocal: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18390 ave 18390 max 18390 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: 769668 ave 769668 max 769668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 769668 Ave neighs/atom = 657.836 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 = 6 21 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3405.9849 0 -3405.9849 -3012.0312 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1170 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: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18469 ave 18469 max 18469 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: 773700 ave 773700 max 773700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773700 Ave neighs/atom = 661.282 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) = 10.95 | 10.95 | 10.95 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 -3405.9849 -3405.9849 34.656919 138.78038 4.0154372 -3012.0312 -3012.0312 -2.1134357 -9032.4091 -1.570945 2.5553457 336.40826 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1170 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: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18469 ave 18469 max 18469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 386850 ave 386850 max 386850 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 773700 ave 773700 max 773700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 773700 Ave neighs/atom = 661.282 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_071.0754/numatoms.out 1170 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3405.98491272067-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3405.98491272067-1170*${isolated_atom_energy} variable adjusted_pe_metal equal -3405.98491272067-1170*0 print "${adjusted_pe_metal} eV" file output/dump_071.0754/energy.out -3405.98491272067 eV print "${mindist_metal} Angstroms" file output/dump_071.0754/mindistance.out 2.55534567734471 Angstroms write_dump all cfg output/dump_071.0754/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_071.0754/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:49