154 lines
4.8 KiB
Plaintext
154 lines
4.8 KiB
Plaintext
LAMMPS (19 Mar 2020)
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# Demonstrate SNAP Ta potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 1
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variable a equal 3.1803
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 1
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variable ny equal ${nrep}
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variable ny equal 1
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variable nz equal ${nrep}
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variable nz equal 1
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boundary p p p
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lattice bcc $a
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lattice bcc 3.1803
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Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 1 0 ${ny} 0 ${nz}
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region box block 0 1 0 1 0 ${nz}
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region box block 0 1 0 1 0 1
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create_box 1 box
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Created orthogonal box = (0 0 0) to (3.1803 3.1803 3.1803)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 2 atoms
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create_atoms CPU = 0.000215 secs
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displace_atoms all random 0.01 0.01 0.01 12345
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mass 1 183.84
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# choose potential
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include W.snap.quadratic
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#
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#
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# Definition of SNAP+ZBL potential.
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 74
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# Specify hybrid with SNAP and ZBL
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pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
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pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
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pair_style hybrid/overlay zbl 4 4.8 snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff 1 1 zbl 74 ${zblz}
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pair_coeff 1 1 zbl 74 74
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pair_coeff * * snap W.quadratic.snapcoeff W.quadratic.snapparam W
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SNAP Element = W, Radius 0.5, Weight 1
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SNAP keyword rcutfac 4.73442
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SNAP keyword twojmax 6
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 1
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SNAP keyword quadraticflag 1
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# Setup 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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dump 1 all custom 100 dump.quadratic.* id type fx fy fz c_eatom
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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 no
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# Run MD
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velocity all create 300.0 4928459
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fix 1 all nve
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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 no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.8
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ghost atom cutoff = 5.8
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binsize = 2.9, bins = 2 2 2
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair zbl, perpetual, half/full from (2)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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(2) pair snap, 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) = 7.284 | 7.284 | 7.284 Mbytes
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Step Temp E_pair c_energy TotEng Press v_press
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0 300 -1.1575362 -1.1575362 -1.1381472 600966 -600966
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10 349.32287 -1.1607243 -1.1607243 -1.1381475 599985.48 -599985.48
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20 384.27065 -1.1629832 -1.1629832 -1.1381478 599287.89 -599287.89
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30 399.34846 -1.1639578 -1.1639578 -1.1381478 598986.42 -598986.42
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40 392.19413 -1.1634953 -1.1634953 -1.1381478 599130.05 -599130.05
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50 363.93932 -1.161669 -1.161669 -1.1381476 599694.93 -599694.93
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60 319.03014 -1.1587663 -1.1587663 -1.1381473 600588.89 -600588.89
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70 264.53512 -1.1552439 -1.1552439 -1.138147 601667.76 -601667.76
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80 209.04294 -1.1516571 -1.1516571 -1.1381466 602760.01 -602760.01
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90 161.3157 -1.1485722 -1.1485722 -1.1381463 603694.49 -603694.49
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100 128.9054 -1.1464773 -1.1464773 -1.1381461 604326.7 -604326.7
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Loop time of 0.030198 on 1 procs for 100 steps with 2 atoms
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Performance: 143.056 ns/day, 0.168 hours/ns, 3311.478 timesteps/s
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98.4% CPU use with 1 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 | 0.028723 | 0.028723 | 0.028723 | 0.0 | 95.12
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Neigh | 0.000515 | 0.000515 | 0.000515 | 0.0 | 1.71
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Comm | 0.000263 | 0.000263 | 0.000263 | 0.0 | 0.87
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Output | 0.000618 | 0.000618 | 0.000618 | 0.0 | 2.05
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Modify | 2.7e-05 | 2.7e-05 | 2.7e-05 | 0.0 | 0.09
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Other | | 5.2e-05 | | | 0.17
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Nlocal: 2 ave 2 max 2 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 187 ave 187 max 187 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 58 ave 58 max 58 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 116 ave 116 max 116 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 116
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Ave neighs/atom = 58
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Neighbor list builds = 100
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Dangerous builds not checked
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Total wall time: 0:00:00
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