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