229 lines
9.7 KiB
Plaintext
229 lines
9.7 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 -8 8 -3 3 -3 3
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region mdRegion block -6 6 -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 atomRegion
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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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pair_style lj/cut 13.
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#pair_coeff 1 1 0.010323166 3.405 13.5
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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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# 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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# 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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fix_modify AtC time_integration fractional_step
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fix_modify AtC internal_atom_integrate off
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fix iNVE internal nve
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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 displacement x lbc 0.
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fix_modify AtC fix velocity x lbc 0.
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# specify atom types
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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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fix_modify AtC internal_quadrature off
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fix_modify AtC control localized_lambda on
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fix_modify AtC control momentum flux interpolate
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#fix_modify AtC control momentum hoover # tested in this mode
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#fix_modify AtC filter type exponential
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#fix_modify AtC filter scale 1000.0
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#fix_modify AtC filter on
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# run to extension
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#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
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#dump D1 all atom 50 bar1d_frac_step_init.dmp
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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 = 65.169 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -4509.8851 0 -4509.8851 26.948349
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100 4.7374019e-13 -4509.8851 0 -4509.8851 26.94834
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200 9.7683427e-13 -4509.8851 0 -4509.8851 26.94803
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300 1.9565172e-11 -4509.8851 0 -4509.8851 26.946439
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400 2.6411547e-10 -4509.8852 0 -4509.8852 26.942798
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500 1.351766e-09 -4509.8852 0 -4509.8852 26.93773
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600 3.6802148e-09 -4509.8852 0 -4509.8852 26.932648
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700 6.6530697e-09 -4509.8852 0 -4509.8852 26.928033
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800 9.5474556e-09 -4509.8852 0 -4509.8852 26.923147
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900 1.2412323e-08 -4509.8852 0 -4509.8852 26.917542
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1000 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973
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Loop time of 19.6581 on 4 procs for 1000 steps with 2304 atoms
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Pair time (%) = 5.96992 (30.3688)
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Neigh time (%) = 2.49911 (12.7129)
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Comm time (%) = 6.03219 (30.6855)
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Outpt time (%) = 0.000867546 (0.00441317)
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Other time (%) = 5.15602 (26.2285)
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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 288910 max 68513 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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# reset time
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fix_modify AtC reset_time 0.
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reset_timestep 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_frac_stepFE 500 text #binary
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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#fix_modify AtC output index step
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#undump D1
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#dump D1 all atom 500 bar1d_frac_step.dmp
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# run to equilibrium
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timestep 5
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thermo 100
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run 5000
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Setting up run ...
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Memory usage per processor = 65.169 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973
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100 1.809994e-08 -4509.8852 0 -4509.8852 26.907429
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200 1.9777109e-08 -4509.8852 0 -4509.8852 26.904241
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300 2.0275205e-08 -4509.8852 0 -4509.8852 26.902912
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400 1.9266773e-08 -4509.8852 0 -4509.8852 26.904281
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500 1.6821974e-08 -4509.8851 0 -4509.8851 26.908126
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600 1.370661e-08 -4509.8852 0 -4509.8852 26.912761
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700 1.0292223e-08 -4509.8852 0 -4509.8852 26.916838
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800 6.5498338e-09 -4509.8853 0 -4509.8853 26.920715
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900 3.1643856e-09 -4509.8853 0 -4509.8853 26.925094
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1000 1.0112513e-09 -4509.8852 0 -4509.8852 26.928958
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1100 4.4564547e-10 -4509.8852 0 -4509.8852 26.930177
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1200 2.264627e-09 -4509.8852 0 -4509.8852 26.92803
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1300 6.3325706e-09 -4509.8853 0 -4509.8853 26.923952
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1400 1.1281983e-08 -4509.8853 0 -4509.8853 26.919616
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1500 1.5582979e-08 -4509.8852 0 -4509.8852 26.915411
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1600 1.8378446e-08 -4509.8852 0 -4509.8852 26.911278
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1700 1.9544417e-08 -4509.8852 0 -4509.8852 26.907886
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1800 1.993739e-08 -4509.8851 0 -4509.8851 26.905965
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1900 1.9956722e-08 -4509.8851 0 -4509.8851 26.905229
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2000 1.9225238e-08 -4509.8852 0 -4509.8852 26.905144
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2100 1.6580757e-08 -4509.8853 0 -4509.8853 26.906419
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2200 1.2058028e-08 -4509.8853 0 -4509.8853 26.910376
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2300 7.4549951e-09 -4509.8852 0 -4509.8852 26.916716
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2400 4.0264612e-09 -4509.8852 0 -4509.8852 26.923054
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2500 1.8321195e-09 -4509.8852 0 -4509.8852 26.92718
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2600 5.8894583e-10 -4509.8852 0 -4509.8852 26.92887
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2700 1.1822868e-09 -4509.8853 0 -4509.8853 26.928935
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2800 4.1199827e-09 -4509.8853 0 -4509.8853 26.927485
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2900 8.3401571e-09 -4509.8853 0 -4509.8853 26.924202
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3000 1.2795486e-08 -4509.8852 0 -4509.8852 26.91968
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3100 1.656454e-08 -4509.8852 0 -4509.8852 26.915184
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3200 1.8809835e-08 -4509.8852 0 -4509.8852 26.911167
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3300 1.9524689e-08 -4509.8852 0 -4509.8852 26.907277
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3400 1.9239653e-08 -4509.8852 0 -4509.8852 26.904028
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3500 1.8306513e-08 -4509.8852 0 -4509.8852 26.903155
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3600 1.6715381e-08 -4509.8852 0 -4509.8852 26.905573
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3700 1.4633381e-08 -4509.8851 0 -4509.8851 26.909896
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3800 1.1933216e-08 -4509.8851 0 -4509.8851 26.913983
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3900 8.1608505e-09 -4509.8852 0 -4509.8852 26.917338
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4000 4.081711e-09 -4509.8853 0 -4509.8853 26.920926
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4100 1.5631282e-09 -4509.8853 0 -4509.8853 26.924958
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4200 1.2262219e-09 -4509.8853 0 -4509.8853 26.928167
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4300 2.985009e-09 -4509.8852 0 -4509.8852 26.929352
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4400 6.8933386e-09 -4509.8852 0 -4509.8852 26.928435
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4500 1.1278724e-08 -4509.8852 0 -4509.8852 26.925624
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4600 1.4438096e-08 -4509.8852 0 -4509.8852 26.920742
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4700 1.6779441e-08 -4509.8852 0 -4509.8852 26.914294
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4800 1.8690218e-08 -4509.8853 0 -4509.8853 26.908349
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4900 1.9317873e-08 -4509.8852 0 -4509.8852 26.905059
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5000 1.8273072e-08 -4509.8851 0 -4509.8851 26.904542
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Loop time of 97.2827 on 4 procs for 5000 steps with 2304 atoms
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Pair time (%) = 29.7789 (30.6107)
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Neigh time (%) = 12.5179 (12.8676)
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Comm time (%) = 29.2909 (30.109)
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Outpt time (%) = 0.00928915 (0.00954861)
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Other time (%) = 25.6857 (26.4032)
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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 288957 max 67836 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 = 500
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Dangerous builds = 0
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