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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
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