282 lines
11 KiB
Plaintext
282 lines
11 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style atomic
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# create domain
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#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
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lattice fcc 5.2582305 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
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# create atoms
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region simRegion block -12 12 -3 3 -3 3
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region atomRegion block -9 9 -3 3 -3 3
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region mdRegion block -8 8 -3 3 -3 3
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boundary f p p
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create_box 1 simRegion
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Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
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4 by 1 by 1 MPI processor grid
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create_atoms 1 region mdRegion
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Created 2304 atoms
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mass 1 39.95
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# specify interal/ghost atoms
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region mdInternal block -6 6 -3 3 -3 3
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region leftghost block -8 -6 -3 3 -3 3
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region rightghost block 6 8 -3 3 -3 3
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group internal region mdInternal
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1728 atoms in group internal
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group Lghost region leftghost
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288 atoms in group Lghost
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group Rghost region rightghost
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288 atoms in group Rghost
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group ghosts union Lghost Rghost
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576 atoms in group ghosts
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# velocities have Vcm = 0
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#velocity internal create 40. 87287 mom yes loop geom
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pair_style lj/cut 13.
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#pair_coeff 1 1 0.010323166 3.405 13.
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pair_coeff 1 1 .2381 3.405 13.
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# define layer
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc elastic Ar_elastic.mat
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ATC: constructing elastic coupling with parameter file Ar_elastic.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: computed mass density : 1.09915
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ATC: computed mass density : 1.09915
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ATC: computed mass density : 1.09915
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ATC: 3 materials defined from Ar_elastic.mat
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#fix_modify AtC boundary Lghost
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#fix_modify AtC boundary Rghost
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fix_modify AtC boundary ghosts
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create 12 1 1 simRegion f p p
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ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
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fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
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ATC: created faceset obndy with 2 faces
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# initial conditions
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fix_modify AtC initial displacement x all 0.0
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fix_modify AtC initial displacement y all 0.0
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fix_modify AtC initial displacement z all 0.0
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fix_modify AtC initial velocity x all 0.0
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fix_modify AtC initial velocity y all 0.0
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fix_modify AtC initial velocity z all 0.0
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# set node sets and bcs
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# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
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fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
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ATC: created nodeset lbc with 1 nodes
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fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
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ATC: created nodeset rbc with 1 nodes
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fix_modify AtC fix velocity x rbc 0.00000004
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#fix_modify AtC fix velocity x rbc 0.
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#fix_modify AtC fix displacement x rbc 0.
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fix_modify AtC fix displacement x lbc 0.
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fix_modify AtC fix velocity x lbc 0.
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#fix_modify AtC output follow_ex.fe 50
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fix_modify AtC internal_quadrature off
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#fix_modify AtC control lumped_lambda_solve on
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#fix_modify AtC momentum control glc_velocity
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#fix_modify AtC momentum control flux faceset obndy
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fix_modify AtC control momentum flux interpolate
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#fix_modify AtC filter scale 1000.0
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# run to extension
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compute myTemp internal temp
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compute atomStress internal stress/atom
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compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
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variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
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thermo_style custom step c_myTemp v_myPres pe
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fix_modify AtC output bar1d_fluxFE 10 text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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timestep 5
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thermo 100
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run 1000
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Setting up run ...
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Memory usage per processor = 65.6268 Mbytes
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Step myTemp myPres PotEng
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0 0 -0.00072339042 -4509.8851
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100 1.7485737e-12 -0.00065677838 -4509.8851
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200 2.1209236e-12 -0.00058835409 -4509.8851
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300 3.1757662e-11 -0.00088336321 -4509.8851
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400 4.4437682e-10 -0.0022808215 -4509.8852
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500 2.1276171e-09 -0.0055205162 -4509.8852
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600 5.3746766e-09 -0.010513144 -4509.8852
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700 9.3752238e-09 -0.016165157 -4509.8852
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800 1.3218953e-08 -0.02139071 -4509.8852
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900 1.6753544e-08 -0.026203391 -4509.8852
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1000 2.0559423e-08 -0.031228823 -4509.8852
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Loop time of 20.2117 on 4 procs for 1000 steps with 2304 atoms
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Pair time (%) = 5.83883 (28.8884)
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Neigh time (%) = 2.45972 (12.1698)
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Comm time (%) = 5.73308 (28.3652)
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Outpt time (%) = 0.0113837 (0.0563225)
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Other time (%) = 6.16865 (30.5203)
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Nlocal: 576 ave 864 max 288 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 5170 ave 6910 max 3430 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 178632 ave 288102 max 69229 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 357264 ave 577008 max 137520 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 1429056
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Ave neighs/atom = 620.25
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Neighbor list builds = 100
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Dangerous builds = 0
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# change nodes to fixed
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fix_modify AtC fix velocity x rbc 0.
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fix_modify AtC fix displacement x rbc 0.0002
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fix_modify AtC output bar1d_fluxFE 500 text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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# run to equilibrium
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timestep 5
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thermo 100
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run 10000
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Setting up run ...
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Memory usage per processor = 66.0846 Mbytes
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Step myTemp myPres PotEng
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1000 2.0559423e-08 -0.031228823 -4509.8852
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1100 2.4448613e-08 -0.036521719 -4509.8852
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1200 2.7029986e-08 -0.040978057 -4509.8852
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1300 2.7245337e-08 -0.042998684 -4509.8852
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1400 2.5759549e-08 -0.041645718 -4509.8852
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1500 2.2667557e-08 -0.037303114 -4509.8852
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1600 1.8985753e-08 -0.031463351 -4509.8852
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1700 1.6073802e-08 -0.025662764 -4509.8852
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1800 1.2763714e-08 -0.020737937 -4509.8852
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1900 7.2995795e-09 -0.01675253 -4509.8852
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2000 2.1755431e-09 -0.013533314 -4509.8853
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2100 1.1934319e-09 -0.011450448 -4509.8853
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2200 5.1850465e-09 -0.011687818 -4509.8853
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2300 1.1883622e-08 -0.015251299 -4509.8852
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2400 1.6266667e-08 -0.021397871 -4509.8852
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2500 1.9099042e-08 -0.02792249 -4509.8851
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2600 2.184558e-08 -0.033185039 -4509.8852
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2700 2.4595817e-08 -0.037175923 -4509.8852
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2800 2.6643068e-08 -0.040355693 -4509.8852
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2900 2.6394943e-08 -0.042183343 -4509.8852
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3000 2.3989422e-08 -0.041411974 -4509.8852
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3100 2.0979363e-08 -0.037465063 -4509.8851
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3200 1.7427127e-08 -0.031310189 -4509.8852
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3300 1.3963242e-08 -0.024887233 -4509.8852
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3400 1.0069796e-08 -0.019686777 -4509.8852
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3500 4.9395633e-09 -0.01603797 -4509.8853
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3600 1.5407167e-09 -0.013620537 -4509.8853
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3700 2.5284685e-09 -0.012392513 -4509.8853
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3800 7.790979e-09 -0.012777012 -4509.8852
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3900 1.3465317e-08 -0.015407232 -4509.8852
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4000 1.7796468e-08 -0.02062936 -4509.8852
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4100 2.137127e-08 -0.027628973 -4509.8852
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4200 2.3606809e-08 -0.034315098 -4509.8852
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4300 2.5221837e-08 -0.038703928 -4509.8852
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4400 2.6247664e-08 -0.040548555 -4509.8852
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4500 2.5017987e-08 -0.040839998 -4509.8852
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4600 2.1628404e-08 -0.040012148 -4509.8852
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4700 1.7878834e-08 -0.037370745 -4509.8851
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4800 1.5934582e-08 -0.032277925 -4509.8851
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4900 1.2990149e-08 -0.025549108 -4509.8852
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5000 7.8316754e-09 -0.01918358 -4509.8853
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5100 3.3266953e-09 -0.014887033 -4509.8853
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5200 1.805252e-09 -0.01286358 -4509.8853
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5300 4.2912871e-09 -0.012392579 -4509.8852
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5400 9.9026848e-09 -0.013257092 -4509.8852
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5500 1.6165255e-08 -0.015976619 -4509.8852
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5600 2.1206295e-08 -0.020907339 -4509.8852
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5700 2.4000025e-08 -0.027469529 -4509.8852
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5800 2.5521345e-08 -0.034321126 -4509.8852
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5900 2.5894586e-08 -0.039670766 -4509.8852
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6000 2.5086791e-08 -0.042046228 -4509.8852
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6100 2.360407e-08 -0.041352366 -4509.8852
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6200 1.9586346e-08 -0.038824048 -4509.8852
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6300 1.6684228e-08 -0.035608606 -4509.8852
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6400 1.4893508e-08 -0.031584998 -4509.8852
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6500 1.1127507e-08 -0.026164353 -4509.8852
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6600 5.9884577e-09 -0.019764802 -4509.8853
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6700 2.2391294e-09 -0.014210542 -4509.8853
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6800 2.7797654e-09 -0.011431487 -4509.8853
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6900 6.7664929e-09 -0.011810438 -4509.8852
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7000 1.1980057e-08 -0.014206493 -4509.8852
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7100 1.7989445e-08 -0.017536849 -4509.8852
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7200 2.3218176e-08 -0.02190877 -4509.8852
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7300 2.5628573e-08 -0.027653206 -4509.8852
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7400 2.610839e-08 -0.034000347 -4509.8852
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7500 2.4944322e-08 -0.039281243 -4509.8852
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7600 2.2693765e-08 -0.042058723 -4509.8852
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7700 1.9767428e-08 -0.041825858 -4509.8851
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7800 1.6504232e-08 -0.039030684 -4509.8851
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7900 1.4309561e-08 -0.03485307 -4509.8852
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8000 1.3055145e-08 -0.030357952 -4509.8852
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8100 9.5625542e-09 -0.025706075 -4509.8852
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8200 4.6410355e-09 -0.02054295 -4509.8853
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8300 3.2795872e-09 -0.015185677 -4509.8853
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8400 5.509246e-09 -0.011181309 -4509.8853
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8500 9.2654236e-09 -0.010336847 -4509.8852
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8600 1.5169111e-08 -0.013152226 -4509.8852
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8700 2.1124719e-08 -0.018237266 -4509.8852
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8800 2.5607376e-08 -0.023635507 -4509.8852
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8900 2.7829768e-08 -0.028664368 -4509.8853
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9000 2.7490864e-08 -0.033752079 -4509.8853
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9100 2.4629425e-08 -0.038717883 -4509.8852
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9200 1.9856317e-08 -0.042074213 -4509.8851
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9300 1.5754223e-08 -0.042397751 -4509.8851
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9400 1.4158011e-08 -0.039645985 -4509.8851
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9500 1.293562e-08 -0.034905375 -4509.8852
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9600 1.0925115e-08 -0.029498287 -4509.8852
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9700 8.2117111e-09 -0.024274276 -4509.8853
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9800 4.2073503e-09 -0.019498803 -4509.8853
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9900 3.6200071e-09 -0.015198764 -4509.8853
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10000 7.3205984e-09 -0.011878546 -4509.8852
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10100 1.2327605e-08 -0.010695702 -4509.8852
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10200 1.7930358e-08 -0.012691556 -4509.8852
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10300 2.4534101e-08 -0.017839785 -4509.8852
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10400 2.8574489e-08 -0.024561434 -4509.8852
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10500 2.944535e-08 -0.030655475 -4509.8852
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10600 2.7962098e-08 -0.034958095 -4509.8852
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10700 2.3119076e-08 -0.037998711 -4509.8852
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10800 1.684499e-08 -0.040493081 -4509.8852
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10900 1.2305474e-08 -0.041691151 -4509.8851
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11000 1.1330272e-08 -0.040137729 -4509.8851
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Loop time of 198.827 on 4 procs for 10000 steps with 2304 atoms
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Pair time (%) = 58.1282 (29.2355)
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Neigh time (%) = 24.4055 (12.2747)
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Comm time (%) = 55.6289 (27.9785)
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Outpt time (%) = 0.0868983 (0.0437054)
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Other time (%) = 60.5779 (30.4676)
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Nlocal: 576 ave 864 max 288 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 5170 ave 6910 max 3430 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 178632 ave 288705 max 68731 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 357264 ave 577008 max 137520 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 1429056
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Ave neighs/atom = 620.25
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Neighbor list builds = 1000
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Dangerous builds = 0
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