forked from lijiext/lammps
212 lines
7.5 KiB
Plaintext
212 lines
7.5 KiB
Plaintext
LAMMPS (30 Aug 2013)
|
|
|
|
units real
|
|
atom_style atomic
|
|
|
|
# create domain
|
|
#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)
|
|
lattice fcc 5.2582305 origin 0.25 0.25 0.25
|
|
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
|
|
|
|
region simRegion block -12 12 -3 3 -3 3
|
|
region mdRegion block -8 8 -3 3 -3 3
|
|
boundary f p p
|
|
create_box 1 simRegion
|
|
Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
|
|
4 by 1 by 1 MPI processor grid
|
|
create_atoms 1 region mdRegion
|
|
Created 2304 atoms
|
|
mass 1 39.95
|
|
|
|
# specify interal/ghost atoms
|
|
region mdInternal block -6 6 -3 3 -3 3
|
|
region leftghost block -8 -6 -3 3 -3 3
|
|
region rightghost block 6 8 -3 3 -3 3
|
|
group internal region mdInternal
|
|
1728 atoms in group internal
|
|
group Lghost region leftghost
|
|
288 atoms in group Lghost
|
|
group Rghost region rightghost
|
|
288 atoms in group Rghost
|
|
group ghosts union Lghost Rghost
|
|
576 atoms in group ghosts
|
|
|
|
# velocities have Vcm = 0, NOTE next for lines commented out for restart
|
|
pair_style lj/cut 13.
|
|
#pair_coeff 1 1 0.010323166 3.405 13.
|
|
pair_coeff 1 1 .2381 3.405 13.
|
|
|
|
neighbor 5. bin
|
|
neigh_modify every 10 delay 0 check no
|
|
|
|
# define layer
|
|
# ID group atc PhysicsType ParameterFile
|
|
fix AtC internal atc elastic Ar_elastic.mat
|
|
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
|
|
ATC: version 2.0
|
|
ATC: peratom PE compute created with ID: 3
|
|
ATC: computed mass density : 1.09915
|
|
ATC: computed mass density : 1.09915
|
|
ATC: computed mass density : 1.09915
|
|
ATC: 3 materials defined from Ar_elastic.mat
|
|
fix_modify AtC boundary ghosts
|
|
|
|
# ID part keywords nx ny nz region
|
|
fix_modify AtC mesh create 12 1 1 simRegion f p p
|
|
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
|
|
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
|
|
ATC: created faceset obndy with 2 faces
|
|
fix_modify AtC internal_quadrature off
|
|
fix_modify AtC internal_atom_integrate off
|
|
fix iNVE internal nve
|
|
|
|
# initial conditions
|
|
fix_modify AtC initial displacement x all 0.0
|
|
fix_modify AtC fix displacement y all 0.0
|
|
fix_modify AtC fix displacement z all 0.0
|
|
fix_modify AtC initial velocity x all 0.0
|
|
fix_modify AtC fix velocity y all 0.0
|
|
fix_modify AtC fix velocity z all 0.0
|
|
|
|
# set node sets and bcs
|
|
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
|
|
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
|
|
ATC: created nodeset lbc with 1 nodes
|
|
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
|
|
ATC: created nodeset rbc with 1 nodes
|
|
#fix_modify AtC fix velocity x rbc 0.
|
|
#fix_modify AtC fix displacement x rbc 0.
|
|
fix_modify AtC fix displacement x lbc 0.
|
|
fix_modify AtC fix velocity x lbc 0.
|
|
|
|
# turn on multiscale
|
|
fix_modify AtC control momentum ghost_flux
|
|
|
|
# new boundary conditions
|
|
fix_modify AtC fix velocity x rbc 0.00000004
|
|
|
|
|
|
#fix_modify AtC output follow_ex.fe 50
|
|
#fix_modify AtC localized_lambda on
|
|
#fix_modify AtC momentum control glc_velocity
|
|
#fix_modify AtC momentum control flux faceset obndy
|
|
#fix_modify AtC control momentum flux
|
|
#fix_modify AtC control momentum ghost_flux
|
|
#fix_modify AtC filter scale 1000.0
|
|
|
|
# run to extension
|
|
compute myTemp internal temp
|
|
compute atomStress internal stress/atom
|
|
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
|
|
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
|
|
thermo_style custom step c_myTemp v_myPres pe
|
|
fix_modify AtC output bar1d_ghost_fluxFE 500 text
|
|
ATC: Warning : text output can create _LARGE_ files
|
|
ATC: output custom names:
|
|
|
|
#dump D1 all atom 100 bar1d_ghost_flux.dmp
|
|
timestep 5
|
|
thermo 100
|
|
run 1000
|
|
Setting up run ...
|
|
Memory usage per processor = 65.6268 Mbytes
|
|
Step myTemp myPres PotEng
|
|
0 0 -0.00072339042 -4509.8851
|
|
100 7.1225566e-14 -0.00069609188 -4509.8851
|
|
200 3.7853133e-13 -0.00065829543 -4509.8851
|
|
300 1.6363911e-11 -0.00093014878 -4509.8851
|
|
400 2.6679578e-10 -0.0022162027 -4509.8852
|
|
500 1.616056e-09 -0.0053039586 -4509.8852
|
|
600 5.0333459e-09 -0.010270696 -4509.8852
|
|
700 9.7370581e-09 -0.016093983 -4509.8852
|
|
800 1.3809125e-08 -0.021486202 -4509.8852
|
|
900 1.6783957e-08 -0.026147268 -4509.8852
|
|
1000 1.9615527e-08 -0.030744945 -4509.8852
|
|
Loop time of 18.3775 on 4 procs for 1000 steps with 2304 atoms
|
|
|
|
Pair time (%) = 5.94283 (32.3375)
|
|
Neigh time (%) = 2.46573 (13.4171)
|
|
Comm time (%) = 6.00265 (32.663)
|
|
Outpt time (%) = 0.00820392 (0.044641)
|
|
Other time (%) = 3.95812 (21.5378)
|
|
|
|
Nlocal: 576 ave 864 max 288 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 5170 ave 6910 max 3430 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Neighs: 178632 ave 288581 max 68542 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
FullNghs: 357264 ave 577008 max 137520 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 1429056
|
|
Ave neighs/atom = 620.25
|
|
Neighbor list builds = 100
|
|
Dangerous builds = 0
|
|
|
|
# change nodes to fixed
|
|
fix_modify AtC unfix velocity x rbc
|
|
#fix_modify AtC fix displacement x rbc 0.0002
|
|
|
|
#fix_modify AtC output bar1d_fluxFE 500 text binary
|
|
|
|
# run to equilibrium
|
|
timestep 5
|
|
thermo 100
|
|
run 3000
|
|
Setting up run ...
|
|
Memory usage per processor = 66.0846 Mbytes
|
|
Step myTemp myPres PotEng
|
|
1000 1.9615527e-08 -0.030744945 -4509.8852
|
|
1100 2.3080841e-08 -0.035570103 -4509.8852
|
|
1200 2.6803382e-08 -0.039749355 -4509.8852
|
|
1300 2.8836885e-08 -0.041881649 -4509.8852
|
|
1400 2.7038886e-08 -0.04118176 -4509.8852
|
|
1500 2.247439e-08 -0.037776265 -4509.8852
|
|
1600 1.8021787e-08 -0.032491325 -4509.8852
|
|
1700 1.4774855e-08 -0.026754505 -4509.8852
|
|
1800 1.2061023e-08 -0.022034601 -4509.8852
|
|
1900 8.5768539e-09 -0.018709001 -4509.8852
|
|
2000 3.6373058e-09 -0.016114748 -4509.8852
|
|
2100 5.3669536e-10 -0.014163462 -4509.8853
|
|
2200 3.2454928e-09 -0.014205399 -4509.8853
|
|
2300 1.030702e-08 -0.017492992 -4509.8853
|
|
2400 1.6038797e-08 -0.023210717 -4509.8852
|
|
2500 1.7061988e-08 -0.029013462 -4509.8851
|
|
2600 1.9296258e-08 -0.03339452 -4509.8852
|
|
2700 2.2816944e-08 -0.036626152 -4509.8852
|
|
2800 2.6944075e-08 -0.039307649 -4509.8852
|
|
2900 2.8170813e-08 -0.040972921 -4509.8852
|
|
3000 2.7256286e-08 -0.040327211 -4509.8852
|
|
3100 2.445985e-08 -0.036617618 -4509.8852
|
|
3200 1.8787648e-08 -0.03049195 -4509.8852
|
|
3300 1.4750104e-08 -0.023629006 -4509.8852
|
|
3400 1.3515772e-08 -0.017473229 -4509.8852
|
|
3500 1.157919e-08 -0.012114855 -4509.8851
|
|
3600 9.6213234e-09 -0.0064144434 -4509.8851
|
|
3700 9.1781574e-09 0.00062376196 -4509.8851
|
|
3800 9.0938842e-09 0.0087100206 -4509.885
|
|
3900 7.7454581e-09 0.016669158 -4509.885
|
|
4000 9.3314606e-09 0.023405906 -4509.885
|
|
Loop time of 54.728 on 4 procs for 3000 steps with 2304 atoms
|
|
|
|
Pair time (%) = 17.812 (32.5465)
|
|
Neigh time (%) = 7.39237 (13.5075)
|
|
Comm time (%) = 17.7536 (32.4397)
|
|
Outpt time (%) = 0.0253569 (0.0463326)
|
|
Other time (%) = 11.7446 (21.46)
|
|
|
|
Nlocal: 576 ave 864 max 288 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 5170 ave 6910 max 3430 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Neighs: 178632 ave 288933 max 68141 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
FullNghs: 357264 ave 577008 max 137520 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 1429056
|
|
Ave neighs/atom = 620.25
|
|
Neighbor list builds = 300
|
|
Dangerous builds = 0
|