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 4.032082897424699*${_u_distance} variable lattice_constant_converted equal 4.032082897424699*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 61.01648613776763*${_u_distance} variable xmax_converted equal 61.01648613776763*1 variable ymin_converted equal -61.02051822066505*${_u_distance} variable ymin_converted equal -61.02051822066505*1 variable ymax_converted equal 61.02051822066505*${_u_distance} variable ymax_converted equal 61.02051822066505*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032082897424699*${_u_distance} variable zmax_converted equal 4.032082897424699*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0320828974247 Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 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 61.0164861377676 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.0164861377676 -61.0205182206651 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.0164861377676 -61.0205182206651 61.0205182206651 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.0164861377676 -61.0205182206651 61.0205182206651 0 ${zmax_converted} units box region whole block 0 61.0164861377676 -61.0205182206651 61.0205182206651 0 4.0320828974247 units box create_box 2 whole Created orthogonal box = (0 -61.0205 0) to (61.0165 61.0205 4.03208) 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 61.0205182206651 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 15 -2 0 orient y 2 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.52961 4.52961 4.03208 create_atoms 1 region upper Created 918 atoms create_atoms CPU = 0.00022912 secs group upper type 1 918 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.8097356776897 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.0205182206651 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 2 0 orient y -2 15 0 orient z 0 0 1 lattice fcc 4.0320828974247 orient x 15 2 0 orient y -2 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.52961 4.52961 4.03208 create_atoms 2 region lower Created 918 atoms create_atoms CPU = 0.000123978 secs group lower type 2 918 atoms in group lower displace_atoms lower move -6.8097356776897 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002 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*4.0320828974247 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01604144871235 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 17 33 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1810 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 17 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.57 | 5.57 | 5.57 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6049.8978 0 -6049.8978 435.33179 289 0 -6065.2085 0 -6065.2085 -5509.0519 Loop time of 2.45743 on 1 procs for 289 steps with 1810 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6049.89779539 -6065.20852116 -6065.20852116 Force two-norm initial, final = 18.8489 3.23214e-06 Force max component initial, final = 4.59632 5.73242e-07 Final line search alpha, max atom move = 1 5.73242e-07 Iterations, force evaluations = 289 572 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3984 | 2.3984 | 2.3984 | 0.0 | 97.60 Neigh | 0.0055382 | 0.0055382 | 0.0055382 | 0.0 | 0.23 Comm | 0.032724 | 0.032724 | 0.032724 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02076 | | | 0.84 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10850 ave 10850 max 10850 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: 196416 ave 196416 max 196416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196416 Ave neighs/atom = 108.517 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) = 5.57 | 5.57 | 5.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume 289 0 -6065.2085 0 -6065.2085 -5509.0519 30024.967 1289 0 -6065.3789 0 -6065.3789 -2010.2206 29890.567 Loop time of 9.44879 on 1 procs for 1000 steps with 1810 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 = -6065.20852116 -6065.3788747 -6065.37887483 Force two-norm initial, final = 104.854 0.0377188 Force max component initial, final = 80.3168 0.0322363 Final line search alpha, max atom move = 0.0810769 0.00261362 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9446 | 8.9446 | 8.9446 | 0.0 | 94.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1097 | 0.1097 | 0.1097 | 0.0 | 1.16 Output | 1.9789e-05 | 1.9789e-05 | 1.9789e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3945 | | | 4.18 Nlocal: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10785 ave 10785 max 10785 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: 198400 ave 198400 max 198400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198400 Ave neighs/atom = 109.613 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 17 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.708 | 5.708 | 5.708 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6065.3789 0 -6065.3789 -2010.2206 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1810 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: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10811 ave 10811 max 10811 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: 206436 ave 206436 max 206436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206436 Ave neighs/atom = 114.053 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) = 5.708 | 5.708 | 5.708 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 -6065.3789 -6065.3789 60.837265 122.04104 4.0258592 -2010.2206 -2010.2206 0.91967686 -6029.8564 -1.7252416 2.5277913 727.10434 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1810 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: 1810 ave 1810 max 1810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10811 ave 10811 max 10811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103218 ave 103218 max 103218 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206436 ave 206436 max 206436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206436 Ave neighs/atom = 114.053 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_015.1893/numatoms.out 1810 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6065.37887482566-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6065.37887482566-1810*${isolated_atom_energy} variable adjusted_pe_metal equal -6065.37887482566-1810*0 print "${adjusted_pe_metal} eV" file output/dump_015.1893/energy.out -6065.37887482566 eV print "${mindist_metal} Angstroms" file output/dump_015.1893/mindistance.out 2.52779134620679 Angstroms write_dump all cfg output/dump_015.1893/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_015.1893/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12