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msvbd
2021-04-23 15:49:11 +02:00
parent 62f7e97316
commit 2e63d126e3
16 changed files with 72 additions and 80 deletions
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examples/USER/misc/dpd_ext/dpdext/dpdext.data Executable file
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examples/USER/misc/dpd_ext/dpdext/in.dpdext Executable file
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# DPD Fluid
variable T equal 1.0
variable rc equal 1.0
variable rcD equal 1.2
units lj
boundary p p p
atom_style atomic
dimension 3
newton on
comm_modify vel yes
### create box and configuration
variable L equal 5.0
lattice fcc 3.0
region simBox block 0 ${L} 0 ${L} 0 ${L}
create_box 2 simBox
#create_atoms 1 region simBox
create_atoms 1 random 100 132456 simBox
create_atoms 2 random 100 132456 simBox
mass 1 1.0
mass 2 2.0
###
pair_style dpd/ext ${T} ${rc} 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
timestep 0.01
run_style verlet
velocity all create ${T} 68768932
thermo_style custom step time temp press
thermo 500
fix 1 all nve
run 50000
write_data final.data pair ij

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LAMMPS (8 Apr 2021)
# DPD Fluid
variable T equal 1.0
variable rc equal 1.0
variable rcD equal 1.2
units lj
boundary p p p
atom_style atomic
dimension 3
newton on
comm_modify vel yes
### create box and configuration
variable L equal 5.0
lattice fcc 3.0
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
region simBox block 0 ${L} 0 ${L} 0 ${L}
region simBox block 0 5 0 ${L} 0 ${L}
region simBox block 0 5 0 5 0 ${L}
region simBox block 0 5 0 5 0 5
create_box 2 simBox
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.5032121 5.5032121 5.5032121)
1 by 1 by 1 MPI processor grid
#create_atoms 1 region simBox
create_atoms 1 random 100 132456 simBox
Created 100 atoms
create_atoms CPU = 0.001 seconds
create_atoms 2 random 100 132456 simBox
Created 100 atoms
create_atoms CPU = 0.000 seconds
mass 1 1.0
mass 2 2.0
###
pair_style dpd/ext ${T} ${rc} 3854262
pair_style dpd/ext 1 ${rc} 3854262
pair_style dpd/ext 1 1 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
timestep 0.01
run_style verlet
velocity all create ${T} 68768932
velocity all create 1 68768932
thermo_style custom step time temp press
thermo 500
fix 1 all nve
run 50000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/ext, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.087 | 3.087 | 3.087 Mbytes
Step Time Temp Press
0 0 1 8.8992215
500 5 0.93699892 8.1219621
1000 10 0.99211009 7.4709658
1500 15 0.91190984 8.828742
2000 20 0.90749036 9.1258378
2500 25 0.97960404 7.085574
3000 30 1.0314836 6.8400202
3500 35 1.0137019 7.2346862
4000 40 0.98189616 6.7265624
4500 45 1.0127497 6.6718402
5000 50 0.90659787 7.4911309
5500 55 1.0257891 6.8163777
6000 60 1.0596209 7.8511522
6500 65 0.95679865 8.4091947
7000 70 1.012617 7.4162991
7500 75 1.0990412 7.160905
8000 80 0.91085269 7.6861008
8500 85 1.1000209 6.4818934
9000 90 0.99982282 8.1312206
9500 95 1.1330979 7.7167159
10000 100 0.98147521 8.4394218
10500 105 1.0254021 7.23574
11000 110 0.94064194 7.9766833
11500 115 1.012364 8.4285752
12000 120 0.94787277 7.0819132
12500 125 1.13729 7.9636837
13000 130 1.1200519 7.1570016
13500 135 0.96797085 8.9794827
14000 140 1.0271217 7.4193307
14500 145 1.0154843 7.3495938
15000 150 1.0408558 7.3047404
15500 155 1.0801685 6.8072764
16000 160 0.9921089 7.3200563
16500 165 0.92952943 7.281934
17000 170 0.87149276 7.6508951
17500 175 0.92808338 6.4774803
18000 180 1.008898 7.1954708
18500 185 0.95962238 8.0257166
19000 190 0.99501354 8.5364854
19500 195 0.97420657 8.3140832
20000 200 0.99926953 7.7840117
20500 205 1.0503096 7.9214552
21000 210 0.97782558 7.4084605
21500 215 0.90363877 7.2867997
22000 220 1.0045369 7.7341956
22500 225 1.0319487 8.4140146
23000 230 1.006863 7.6023442
23500 235 0.90302749 8.0230562
24000 240 1.0768463 7.7315652
24500 245 1.0529241 7.9835388
25000 250 0.96057288 6.9591339
25500 255 0.98941425 7.4287206
26000 260 0.99120107 7.0440907
26500 265 0.94017831 7.9499345
27000 270 0.93766339 8.118634
27500 275 0.98309918 7.9865412
28000 280 1.0191736 8.3330592
28500 285 0.99546328 8.3419405
29000 290 0.95703084 7.313665
29500 295 1.0122694 8.1900103
30000 300 1.0758207 8.2876755
30500 305 1.0981472 6.4742286
31000 310 1.0356215 6.4857599
31500 315 0.95584989 8.4446078
32000 320 1.0591455 8.3936647
32500 325 0.92674627 7.0391747
33000 330 0.93486399 7.6892746
33500 335 1.0772579 7.1395468
34000 340 1.1029975 7.4249835
34500 345 0.9845352 6.3478805
35000 350 1.1004884 8.0179815
35500 355 0.97596833 8.1652441
36000 360 1.0026086 7.8100907
36500 365 1.0242946 7.4683685
37000 370 0.98485255 7.9021959
37500 375 1.078371 8.726722
38000 380 0.99139516 7.3585787
38500 385 1.0531594 8.5221732
39000 390 1.0290073 7.0905003
39500 395 1.0368491 8.0293456
40000 400 1.0520724 7.6372283
40500 405 0.94925657 8.9578914
41000 410 0.99919726 7.7207005
41500 415 1.0507736 6.9924906
42000 420 1.0442899 7.8115665
42500 425 1.0192672 8.5123404
43000 430 0.9784861 8.0556966
43500 435 0.99592222 8.0665153
44000 440 0.95621235 8.4132911
44500 445 0.93400296 7.3266133
45000 450 1.0389454 7.2458003
45500 455 1.1076673 6.5868539
46000 460 1.0826918 7.9286381
46500 465 0.93589963 8.5310745
47000 470 1.0352143 6.6366463
47500 475 1.0497186 8.5074329
48000 480 0.96107226 7.7505527
48500 485 1.1061337 8.2753596
49000 490 1.0337198 7.5777833
49500 495 0.94052507 7.3661443
50000 500 0.98527818 7.1746325
Loop time of 9.88248 on 1 procs for 50000 steps with 200 atoms
Performance: 4371371.882 tau/day, 5059.458 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.7028 | 8.7028 | 8.7028 | 0.0 | 88.06
Neigh | 0.73687 | 0.73687 | 0.73687 | 0.0 | 7.46
Comm | 0.31881 | 0.31881 | 0.31881 | 0.0 | 3.23
Output | 0.0013947 | 0.0013947 | 0.0013947 | 0.0 | 0.01
Modify | 0.081394 | 0.081394 | 0.081394 | 0.0 | 0.82
Other | | 0.04118 | | | 0.42
Nlocal: 200.000 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 547.000 ave 547 max 547 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1651.00 ave 1651 max 1651 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1651
Ave neighs/atom = 8.2550000
Neighbor list builds = 5000
Dangerous builds = 5000
write_data final.data pair ij
System init for write_data ...
Total wall time: 0:00:10

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LAMMPS (8 Apr 2021)
# DPD Fluid
variable T equal 1.0
variable rc equal 1.0
variable rcD equal 1.2
units lj
boundary p p p
atom_style atomic
dimension 3
newton on
comm_modify vel yes
### create box and configuration
variable L equal 5.0
lattice fcc 3.0
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
region simBox block 0 ${L} 0 ${L} 0 ${L}
region simBox block 0 5 0 ${L} 0 ${L}
region simBox block 0 5 0 5 0 ${L}
region simBox block 0 5 0 5 0 5
create_box 2 simBox
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.5032121 5.5032121 5.5032121)
1 by 2 by 2 MPI processor grid
#create_atoms 1 region simBox
create_atoms 1 random 100 132456 simBox
Created 100 atoms
create_atoms CPU = 0.001 seconds
create_atoms 2 random 100 132456 simBox
Created 100 atoms
create_atoms CPU = 0.000 seconds
mass 1 1.0
mass 2 2.0
###
pair_style dpd/ext ${T} ${rc} 3854262
pair_style dpd/ext 1 ${rc} 3854262
pair_style dpd/ext 1 1 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
pair_coeff 2 2 25.2 4.52 4.55 0.52 0.55 1.22 #${rcD}
timestep 0.01
run_style verlet
velocity all create ${T} 68768932
velocity all create 1 68768932
thermo_style custom step time temp press
thermo 500
fix 1 all nve
run 50000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/ext, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.064 | 3.064 Mbytes
Step Time Temp Press
0 0 1 7.9021356
500 5 0.937908 7.0735774
1000 10 0.89467862 7.7074585
1500 15 1.0197239 8.6662041
2000 20 1.0306203 8.0831978
2500 25 0.94106312 7.4609953
3000 30 1.0217162 7.7000536
3500 35 0.9694633 6.9496101
4000 40 0.89886564 7.5844291
4500 45 0.9914389 6.5459858
5000 50 1.0503316 7.1639528
5500 55 0.95397384 7.2900451
6000 60 0.91097079 7.4484481
6500 65 1.0212125 8.6396803
7000 70 0.84788375 9.2247619
7500 75 1.0477577 7.9631111
8000 80 1.0473514 7.2904431
8500 85 1.0482936 7.9668363
9000 90 1.0239558 7.1715815
9500 95 1.0727305 8.2075133
10000 100 0.96755536 7.8062307
10500 105 1.0357222 8.2249507
11000 110 1.053488 6.8283393
11500 115 0.89283913 8.9044509
12000 120 1.0085932 8.1844316
12500 125 0.84259725 6.9608932
13000 130 1.0559908 7.5907714
13500 135 0.95175487 8.8486631
14000 140 0.954129 8.2199072
14500 145 1.0034836 8.6956618
15000 150 0.99411864 7.3723436
15500 155 1.0876662 8.5906664
16000 160 0.98613154 7.6599681
16500 165 1.0355659 6.7243908
17000 170 1.0838802 7.5905171
17500 175 0.95966717 7.3268842
18000 180 0.91267962 8.1126836
18500 185 0.9625394 8.0889468
19000 190 1.0209688 7.2104928
19500 195 0.93315956 8.3484128
20000 200 1.0430989 6.4154856
20500 205 1.037892 7.3727084
21000 210 1.0551654 8.3732908
21500 215 0.97922101 8.0403654
22000 220 1.0480356 9.2304431
22500 225 1.0009668 8.0807868
23000 230 1.0808549 7.9128664
23500 235 0.99282487 7.550466
24000 240 0.96893196 8.0123396
24500 245 0.96945612 6.9129899
25000 250 0.9373397 6.2942852
25500 255 0.98958822 7.8259805
26000 260 0.97971277 7.3263113
26500 265 0.91588062 8.284996
27000 270 1.0045677 7.490418
27500 275 0.92664827 7.2434156
28000 280 0.98527367 7.1695053
28500 285 0.97862372 8.2272887
29000 290 1.067876 8.3157621
29500 295 1.0688998 7.5106281
30000 300 1.117583 8.8135518
30500 305 1.035452 7.3572033
31000 310 1.03275 8.1486503
31500 315 0.96000074 7.6740792
32000 320 0.91763282 7.6603754
32500 325 0.99394287 8.8127132
33000 330 1.0021499 7.9881263
33500 335 0.97639399 8.2361021
34000 340 1.0309313 8.2918535
34500 345 1.0214124 7.3886765
35000 350 1.0029326 8.2745874
35500 355 1.0634485 6.4161924
36000 360 1.0242523 7.4099968
36500 365 1.0302234 8.0604043
37000 370 1.0143945 7.34914
37500 375 0.99553421 6.8818266
38000 380 1.0073546 7.6254332
38500 385 1.0068118 7.4673312
39000 390 0.95181135 6.1644033
39500 395 0.98964849 8.501371
40000 400 0.99441011 8.1515808
40500 405 1.0339683 7.6747037
41000 410 0.99467835 7.8743708
41500 415 1.0231331 7.3169584
42000 420 0.94617359 8.0079888
42500 425 1.0163237 7.7949198
43000 430 0.97039825 8.8842702
43500 435 1.0326956 7.6700965
44000 440 1.1106283 8.2900664
44500 445 0.96697428 7.0408563
45000 450 1.0137186 6.8316108
45500 455 1.0531692 8.0051631
46000 460 1.0382619 7.2937333
46500 465 0.90277459 7.9676952
47000 470 1.00751 8.7594948
47500 475 0.95565907 8.320444
48000 480 1.0396091 7.9262425
48500 485 1.0349892 8.333501
49000 490 0.9759139 7.4839858
49500 495 0.91538068 7.1780491
50000 500 1.0310634 7.1522794
Loop time of 8.5908 on 4 procs for 50000 steps with 200 atoms
Performance: 5028633.375 tau/day, 5820.178 timesteps/s
95.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9505 | 5.054 | 5.1885 | 4.1 | 58.83
Neigh | 0.47025 | 0.47603 | 0.47954 | 0.5 | 5.54
Comm | 2.7876 | 2.9237 | 3.0336 | 5.5 | 34.03
Output | 0.0024114 | 0.0029766 | 0.0046443 | 1.8 | 0.03
Modify | 0.062911 | 0.064188 | 0.065603 | 0.4 | 0.75
Other | | 0.06992 | | | 0.81
Nlocal: 50.0000 ave 53 max 46 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 296.000 ave 301 max 290 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 410.750 ave 431 max 357 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Total # of neighbors = 1643
Ave neighs/atom = 8.2150000
Neighbor list builds = 5000
Dangerous builds = 5000
write_data final.data pair ij
System init for write_data ...
Total wall time: 0:00:08