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lammps/examples/USER/atc/elastic/bar1d_flux.screen
1ca6fb0f8160lammm-master-deprecated

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bar1d_flux.screen
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LAMMPS (24 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
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -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
#velocity internal create 40. 87287 mom yes loop geom
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 Lghost
#fix_modify AtC boundary Rghost
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
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial 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 0.00000004
#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.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#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_fluxFE 10 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
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 1.7485737e-12 -0.00065677838 -4509.8851
200 2.1209236e-12 -0.00058835409 -4509.8851
300 3.1757662e-11 -0.00088336321 -4509.8851
400 4.4437682e-10 -0.0022808215 -4509.8852
500 2.1276171e-09 -0.0055205162 -4509.8852
600 5.3746766e-09 -0.010513144 -4509.8852
700 9.3752238e-09 -0.016165157 -4509.8852
800 1.3218953e-08 -0.02139071 -4509.8852
900 1.6753544e-08 -0.026203391 -4509.8852
1000 2.0559423e-08 -0.031228823 -4509.8852
Loop time of 21.9868 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 6.02817 (27.4173)
Neigh time (%) = 2.55065 (11.6008)
Comm time (%) = 6.10891 (27.7845)
Outpt time (%) = 0.011534 (0.0524588)
Other time (%) = 7.28749 (33.1449)
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 288102 max 69229 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 fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# run to equilibrium
timestep 5
thermo 100
run 10000
Setting up run ...
Memory usage per processor = 66.0846 Mbytes
Step myTemp myPres PotEng
1000 2.0559423e-08 -0.031228823 -4509.8852
1100 2.4448613e-08 -0.036521719 -4509.8852
1200 2.7029986e-08 -0.040978057 -4509.8852
1300 2.7245337e-08 -0.042998684 -4509.8852
1400 2.5759549e-08 -0.041645718 -4509.8852
1500 2.2667557e-08 -0.037303114 -4509.8852
1600 1.8985753e-08 -0.031463351 -4509.8852
1700 1.6073802e-08 -0.025662764 -4509.8852
1800 1.2763714e-08 -0.020737937 -4509.8852
1900 7.2995795e-09 -0.01675253 -4509.8852
2000 2.1755431e-09 -0.013533314 -4509.8853
2100 1.1934319e-09 -0.011450448 -4509.8853
2200 5.1850465e-09 -0.011687818 -4509.8853
2300 1.1883622e-08 -0.015251299 -4509.8852
2400 1.6266667e-08 -0.021397871 -4509.8852
2500 1.9099042e-08 -0.02792249 -4509.8851
2600 2.184558e-08 -0.033185039 -4509.8852
2700 2.4595817e-08 -0.037175923 -4509.8852
2800 2.6643068e-08 -0.040355693 -4509.8852
2900 2.6394943e-08 -0.042183343 -4509.8852
3000 2.3989422e-08 -0.041411974 -4509.8852
3100 2.0979363e-08 -0.037465063 -4509.8851
3200 1.7427127e-08 -0.031310189 -4509.8852
3300 1.3963242e-08 -0.024887233 -4509.8852
3400 1.0069796e-08 -0.019686777 -4509.8852
3500 4.9395633e-09 -0.01603797 -4509.8853
3600 1.5407167e-09 -0.013620537 -4509.8853
3700 2.5284685e-09 -0.012392513 -4509.8853
3800 7.790979e-09 -0.012777012 -4509.8852
3900 1.3465317e-08 -0.015407232 -4509.8852
4000 1.7796468e-08 -0.02062936 -4509.8852
4100 2.137127e-08 -0.027628973 -4509.8852
4200 2.3606809e-08 -0.034315098 -4509.8852
4300 2.5221837e-08 -0.038703928 -4509.8852
4400 2.6247664e-08 -0.040548555 -4509.8852
4500 2.5017987e-08 -0.040839998 -4509.8852
4600 2.1628404e-08 -0.040012148 -4509.8852
4700 1.7878834e-08 -0.037370745 -4509.8851
4800 1.5934582e-08 -0.032277925 -4509.8851
4900 1.2990149e-08 -0.025549108 -4509.8852
5000 7.8316754e-09 -0.01918358 -4509.8853
5100 3.3266953e-09 -0.014887033 -4509.8853
5200 1.805252e-09 -0.01286358 -4509.8853
5300 4.2912871e-09 -0.012392579 -4509.8852
5400 9.9026848e-09 -0.013257092 -4509.8852
5500 1.6165255e-08 -0.015976619 -4509.8852
5600 2.1206295e-08 -0.020907339 -4509.8852
5700 2.4000025e-08 -0.027469529 -4509.8852
5800 2.5521345e-08 -0.034321126 -4509.8852
5900 2.5894586e-08 -0.039670766 -4509.8852
6000 2.5086791e-08 -0.042046228 -4509.8852
6100 2.360407e-08 -0.041352366 -4509.8852
6200 1.9586346e-08 -0.038824048 -4509.8852
6300 1.6684228e-08 -0.035608606 -4509.8852
6400 1.4893508e-08 -0.031584998 -4509.8852
6500 1.1127507e-08 -0.026164353 -4509.8852
6600 5.9884577e-09 -0.019764802 -4509.8853
6700 2.2391294e-09 -0.014210542 -4509.8853
6800 2.7797654e-09 -0.011431487 -4509.8853
6900 6.7664929e-09 -0.011810438 -4509.8852
7000 1.1980057e-08 -0.014206493 -4509.8852
7100 1.7989445e-08 -0.017536849 -4509.8852
7200 2.3218176e-08 -0.02190877 -4509.8852
7300 2.5628573e-08 -0.027653206 -4509.8852
7400 2.610839e-08 -0.034000347 -4509.8852
7500 2.4944322e-08 -0.039281243 -4509.8852
7600 2.2693765e-08 -0.042058723 -4509.8852
7700 1.9767428e-08 -0.041825858 -4509.8851
7800 1.6504232e-08 -0.039030684 -4509.8851
7900 1.4309561e-08 -0.03485307 -4509.8852
8000 1.3055145e-08 -0.030357952 -4509.8852
8100 9.5625542e-09 -0.025706075 -4509.8852
8200 4.6410355e-09 -0.02054295 -4509.8853
8300 3.2795872e-09 -0.015185677 -4509.8853
8400 5.509246e-09 -0.011181309 -4509.8853
8500 9.2654236e-09 -0.010336847 -4509.8852
8600 1.5169111e-08 -0.013152226 -4509.8852
8700 2.1124719e-08 -0.018237266 -4509.8852
8800 2.5607376e-08 -0.023635507 -4509.8852
8900 2.7829768e-08 -0.028664368 -4509.8853
9000 2.7490864e-08 -0.033752079 -4509.8853
9100 2.4629425e-08 -0.038717883 -4509.8852
9200 1.9856317e-08 -0.042074213 -4509.8851
9300 1.5754223e-08 -0.042397751 -4509.8851
9400 1.4158011e-08 -0.039645985 -4509.8851
9500 1.293562e-08 -0.034905375 -4509.8852
9600 1.0925115e-08 -0.029498287 -4509.8852
9700 8.2117111e-09 -0.024274276 -4509.8853
9800 4.2073503e-09 -0.019498803 -4509.8853
9900 3.6200071e-09 -0.015198764 -4509.8853
10000 7.3205984e-09 -0.011878546 -4509.8852
10100 1.2327605e-08 -0.010695702 -4509.8852
10200 1.7930358e-08 -0.012691556 -4509.8852
10300 2.4534101e-08 -0.017839785 -4509.8852
10400 2.8574489e-08 -0.024561434 -4509.8852
10500 2.944535e-08 -0.030655475 -4509.8852
10600 2.7962098e-08 -0.034958095 -4509.8852
10700 2.3119076e-08 -0.037998711 -4509.8852
10800 1.684499e-08 -0.040493081 -4509.8852
10900 1.2305474e-08 -0.041691151 -4509.8851
11000 1.1330272e-08 -0.040137729 -4509.8851
Loop time of 210.662 on 4 procs for 10000 steps with 2304 atoms
Pair time (%) = 59.9967 (28.4801)
Neigh time (%) = 25.1338 (11.9309)
Comm time (%) = 58.7547 (27.8906)
Outpt time (%) = 0.171174 (0.0812552)
Other time (%) = 66.6052 (31.6172)
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 287569 max 69518 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 = 1000
Dangerous builds = 0
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