LAMMPS (27 May 2021) # Run NPT MD simulation for Si at 500 K. variable nsteps index 100 #0 # NOTE: These are not intended to represent real materials units metal atom_style atomic atom_modify map array boundary p p p atom_modify sort 0 0.0 #read_data Si.data lattice diamond 5.43 Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 region box block 0 2 0 2 0 2 create_box 1 box Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 64 atoms create_atoms CPU = 0.000 seconds mass 1 29.0 # temperature variable t equal 500. # Potential #pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor SO3 keyword rcutfac 5.0 SO3 keyword nmax 3 SO3 keyword lmax 4 SO3 keyword alpha 2.0 SO3 keyword nelems 1 SO3 keyword elems Si SO3 keyword radelems 0.5 SO3 keyword welems 14 pair_coeff * * Si Si # Set-up output compute eatom all pe/atom compute energy all reduce sum c_eatom compute satom all stress/atom NULL compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol) thermo_style custom step temp epair c_energy etotal press v_press thermo 10 thermo_modify norm yes # Set up NVE run timestep 0.5e-3 neighbor 1.0 bin neigh_modify once no every 1 delay 0 check yes # Run MD velocity all create $t 5287287 loop geom velocity all create 500 5287287 loop geom fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2 fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2 fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2 run ${nsteps} run 100 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair mliap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 298.2 | 298.2 | 298.2 Mbytes Step Temp E_pair c_energy TotEng Press v_press 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458 Loop time of 1.06231 on 4 procs for 100 steps with 64 atoms Performance: 4.067 ns/day, 5.902 hours/ns, 94.135 timesteps/s 95.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97395 | 1.0072 | 1.048 | 2.7 | 94.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012069 | 0.052803 | 0.086037 | 12.0 | 4.97 Output | 0.00052595 | 0.0005523 | 0.00062776 | 0.0 | 0.05 Modify | 0.0014014 | 0.001442 | 0.0014772 | 0.1 | 0.14 Other | | 0.0003045 | | | 0.03 Nlocal: 16.0000 ave 16 max 16 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 349.000 ave 349 max 349 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 736.000 ave 736 max 736 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2944 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:01