206 lines
7.3 KiB
Plaintext
206 lines
7.3 KiB
Plaintext
LAMMPS (30 Aug 2013)
|
|
units real
|
|
atom_style atomic
|
|
|
|
variable l equal 8
|
|
variable g equal 2
|
|
variable lg equal $l+$g
|
|
variable lg equal 8+$g
|
|
variable lg equal 8+2
|
|
variable w equal 2
|
|
|
|
lattice fcc 5.405 origin 0.25 0.25 0.25
|
|
Lattice spacing in x,y,z = 5.405 5.405 5.405
|
|
boundary f f f
|
|
|
|
# region to create atoms
|
|
region bigCyl cylinder z 0. 0. ${lg} -$w $w
|
|
region bigCyl cylinder z 0. 0. 10 -$w $w
|
|
region bigCyl cylinder z 0. 0. 10 -2 $w
|
|
region bigCyl cylinder z 0. 0. 10 -2 2
|
|
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
|
|
region offsetPlane block -10 $g -${lg} ${lg} -$w $w
|
|
region offsetPlane block -10 2 -${lg} ${lg} -$w $w
|
|
region offsetPlane block -10 2 -10 ${lg} -$w $w
|
|
region offsetPlane block -10 2 -10 10 -$w $w
|
|
region offsetPlane block -10 2 -10 10 -2 $w
|
|
region offsetPlane block -10 2 -10 10 -2 2
|
|
region mdRegion intersect 2 bigCyl offsetPlane
|
|
#create_box 1 mdRegion
|
|
pair_style lj/cut 13.5
|
|
read_data semicircle.init
|
|
Reading data file ...
|
|
orthogonal box = (-54.05 -54.05 -10.81) to (10.81 54.05 10.81)
|
|
2 by 2 by 1 MPI processor grid
|
|
3168 atoms
|
|
3168 velocities
|
|
|
|
# region for internal atoms
|
|
region mdInternalCyl cylinder z 0. 0. $l -$w $w
|
|
region mdInternalCyl cylinder z 0. 0. 8 -$w $w
|
|
region mdInternalCyl cylinder z 0. 0. 8 -2 $w
|
|
region mdInternalCyl cylinder z 0. 0. 8 -2 2
|
|
region leftHalfPlane block INF 0. INF INF INF INF
|
|
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
|
|
|
|
# region for coupling ghosts
|
|
region rightHalfPlane block 0. INF INF INF INF INF
|
|
region mdGhost union 2 rightHalfPlane mdInternal side out
|
|
|
|
#create_atoms 1 region mdRegion
|
|
#create_atoms 1 region mdInternal
|
|
#create_atoms 2 region mdGhost
|
|
#region outerGhost intersect 2 rightHalfPlane mdRegion
|
|
#create_atoms 3 region outerGhost
|
|
|
|
#pair_style lj/cut 13.5
|
|
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
|
|
#mass 1 39.95
|
|
#pair_coeff 1 1 .238 3.405 13.5
|
|
group internal region mdInternal
|
|
1624 atoms in group internal
|
|
group ghost region mdGhost
|
|
904 atoms in group ghost
|
|
#velocity internal create 40 102486 mom yes rot yes dist gaussian
|
|
#write_restart semicircle_init.rst
|
|
|
|
# ATC commands
|
|
fix AtC internal atc thermal Ar_ttm.mat
|
|
ATC: constructing thermal coupling with parameter file Ar_ttm.mat
|
|
ATC: version 2.0
|
|
ATC: peratom PE compute created with ID: 3
|
|
ATC: 2 materials defined from Ar_ttm.mat
|
|
fix_modify AtC boundary ghost
|
|
fix_modify AtC mesh read semicircle.mesh f f p
|
|
ATC: read 398 nodes
|
|
ATC: read 176 HEX8 elements
|
|
ATC: P1, writing periodicity corrected mesh: periodic_semicircle.mesh
|
|
ATC: P3, writing periodicity corrected mesh: periodic_semicircle.mesh
|
|
ATC: condensed 199 periodic nodes in the 3 direction
|
|
ATC: created nodeset 1 with 44 nodes
|
|
ATC: created nodeset 2 with 4 nodes
|
|
ATC: P2, writing periodicity corrected mesh: periodic_semicircle.mesh
|
|
ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
|
|
ATC: P0, writing periodicity corrected mesh: periodic_semicircle.mesh
|
|
fix_modify AtC mesh nodeset_to_elementset 2 hole min
|
|
fix_modify AtC internal_quadrature off
|
|
fix_modify AtC time_integration fractional_step
|
|
|
|
# initial conditions
|
|
fix_modify AtC fix temperature all 20.
|
|
fix_modify AtC control thermal rescale 10
|
|
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
|
|
|
|
# initial output
|
|
#fix_modify AtC mesh output semicircle_mesh
|
|
#fix_modify AtC output semicircle_init 100 text binary
|
|
#dump D1 all atom 100 semicircle_init.dmp
|
|
|
|
# run
|
|
timestep 5.0
|
|
thermo 100
|
|
run 500
|
|
Setting up run ...
|
|
Memory usage per processor = 52.3462 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 20.498895 -5250.6971 0 -5057.1829 -1088.0506
|
|
100 10.255763 -5131.7808 0 -5034.9641 -671.92179
|
|
200 10.255763 -5194.8934 0 -5098.0766 -664.20614
|
|
300 10.255763 -5191.6455 0 -5094.8288 -564.44341
|
|
400 10.255763 -5185.5031 0 -5088.6864 -611.34498
|
|
500 10.255763 -5185.1021 0 -5088.2853 -686.81479
|
|
Loop time of 9.08358 on 4 procs for 500 steps with 3168 atoms
|
|
|
|
Pair time (%) = 2.5019 (27.5431)
|
|
Neigh time (%) = 0.0543029 (0.597814)
|
|
Comm time (%) = 0.724279 (7.97349)
|
|
Outpt time (%) = 0.000456929 (0.00503028)
|
|
Other time (%) = 5.80264 (63.8806)
|
|
|
|
Nlocal: 792 ave 944 max 640 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 860 ave 888 max 832 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Neighs: 95743.8 ave 114417 max 76793 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
FullNghs: 191488 ave 228943 max 153856 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 765950
|
|
Ave neighs/atom = 241.777
|
|
Neighbor list builds = 5
|
|
Dangerous builds = 0
|
|
|
|
# boundary conditions
|
|
fix_modify AtC unfix temperature all
|
|
fix_modify AtC fix temperature 1 20.
|
|
fix_modify AtC control thermal flux
|
|
fix_modify AtC control localized_lambda on
|
|
|
|
# NOTE appears to be a problem with the temporal ramp function
|
|
variable delta_t equal 1000*5.
|
|
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
|
|
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 5000
|
|
|
|
# equilibrate filter
|
|
fix_modify AtC filter type exponential
|
|
fix_modify AtC filter scale 1000.
|
|
fix_modify AtC filter on
|
|
|
|
# equilibration output
|
|
fix_modify AtC output semicircleFE 100 full_text #binary
|
|
ATC: Warning : text output can create _LARGE_ files
|
|
ATC: output custom names:
|
|
|
|
#undump D1
|
|
#dump D1 all atom 100 semicircle_equil.dmp
|
|
|
|
# run
|
|
fix_modify AtC reset_time 0.
|
|
reset_timestep 0
|
|
thermo 100
|
|
run 1000
|
|
Setting up run ...
|
|
Memory usage per processor = 65.9216 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 10.255763 -5185.1021 0 -5088.2853 -686.81479
|
|
100 9.9160769 -5177.6646 0 -5084.0545 -753.44628
|
|
200 10.215779 -5182.5539 0 -5086.1147 -721.64916
|
|
300 10.609664 -5183.8798 0 -5083.7222 -672.99308
|
|
400 10.754797 -5188.6804 0 -5087.1527 -620.77678
|
|
500 10.271869 -5184.1487 0 -5087.18 -643.71337
|
|
600 10.214975 -5184.0211 0 -5087.5894 -687.47365
|
|
700 10.231487 -5182.315 0 -5085.7274 -719.65308
|
|
800 10.245262 -5181.8268 0 -5085.1092 -707.19351
|
|
900 10.342331 -5183.9012 0 -5086.2673 -667.21622
|
|
1000 10.446039 -5184.9612 0 -5086.3482 -647.13367
|
|
Loop time of 25.9666 on 4 procs for 1000 steps with 3168 atoms
|
|
|
|
Pair time (%) = 4.93896 (19.0204)
|
|
Neigh time (%) = 0.0919983 (0.354294)
|
|
Comm time (%) = 1.34195 (5.16797)
|
|
Outpt time (%) = 0.0565627 (0.217828)
|
|
Other time (%) = 19.5372 (75.2395)
|
|
|
|
Nlocal: 792 ave 944 max 640 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Nghost: 860 ave 888 max 832 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
Neighs: 95600.8 ave 114809 max 76836 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
FullNghs: 191202 ave 228917 max 153483 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
|
|
Total # of neighbors = 764806
|
|
Ave neighs/atom = 241.416
|
|
Neighbor list builds = 8
|
|
Dangerous builds = 0
|
|
|
|
# heat source
|
|
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
|
|
#fix_modify AtC source temperature hole 0.0000000001
|
|
#fix_modify AtC output semicircleFE 1 full_text #binary
|
|
#undump D1
|
|
#dump D1 all atom 100 semicircle.dmp
|
|
#run 1#000
|