ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13471 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-05-15 19:36:25 +00:00
parent 723da5079a
commit 07f62aea1a
118 changed files with 20984 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

135
examples/colloid/log.15May15.colloid.g++.1 Normal file
View File

@ -0,0 +1,135 @@
LAMMPS (30 Apr 2015)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
comm_modify mode multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 13.5
Memory usage per processor = 3.86192 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011
2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014
3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78
4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579
5000 2.1407629 0.016107912 2.1544922 0.076141728 28576.1
6000 2.1131357 0.00050904012 2.1112969 0.095060602 21598.175
7000 2.0717026 0.013639823 2.0830406 0.11782618 17864.757
8000 2.0557671 0.015637275 2.0691201 0.13461012 15542.602
9000 2.052181 0.011294709 2.0611955 0.15150744 13852.149
10000 2.0531753 0.005995461 2.0568894 0.17005868 12487.961
11000 2.0458212 0.013960278 2.0575083 0.18853479 11391.15
12000 2.0405323 0.01846093 2.056726 0.20856764 10532.913
13000 2.0169788 0.041436672 2.0561744 0.23593917 9743.2413
14000 2.0381291 0.017030208 2.0528947 0.23907374 9093.804
15000 2.0400498 0.010140701 2.0479238 0.27667462 8571.3248
16000 2.0280005 0.024278921 2.0500261 0.31642444 8133.8701
17000 2.0330813 0.018237365 2.0490597 0.30128788 7764.8228
18000 2.0239878 0.02723825 2.0489771 0.30818234 7455.765
19000 2.0213402 0.035515393 2.0546096 0.39654991 7096.9286
20000 2.024466 0.032163441 2.0543801 0.37550172 6782.3498
21000 2.033932 0.017240839 2.0489129 0.39674508 6520.0345
22000 2.0204921 0.033630164 2.0518773 0.41617948 6306.7194
23000 2.0103922 0.046109389 2.0542679 0.44503939 6108.8439
24000 2.0063543 0.049507774 2.0536328 0.4949354 5923.2093
25000 1.9953872 0.066107231 2.0592773 0.5424389 5746.6695
26000 2.0416248 0.020853398 2.0602097 0.46642685 5593.8186
27000 2.0280574 0.037040684 2.0628447 0.49730884 5433.376
28000 2.0039648 0.055918617 2.0576568 0.56893257 5281.5584
29000 2.0042398 0.056161548 2.0581744 0.55361133 5164.0991
30000 2.031788 0.030776854 2.0603073 0.58478846 5056.2821
31000 2.0220647 0.044025601 2.0638435 0.60571441 4939.9798
32000 2.0115578 0.0548283 2.064151 0.62749615 4859.2601
33000 1.9905768 0.071616735 2.0599817 0.64066244 4787.7818
34000 2.0209823 0.052197269 2.0709341 0.68260584 4705.5825
35000 1.995165 0.078611977 2.0715601 0.69333031 4599.9346
36000 1.994471 0.079545726 2.0718006 0.7510532 4523.7494
37000 1.9939754 0.083417982 2.0751779 0.73746747 4449.8485
38000 1.9808613 0.098188975 2.0768493 0.89305039 4362.0588
39000 2.0056223 0.070537588 2.0739314 0.75049166 4320.201
40000 2.0490165 0.033488307 2.0802281 0.71809099 4259.8017
41000 2.0170375 0.066555481 2.0813519 0.80145545 4165.276
42000 2.034609 0.050123688 2.082472 0.7318767 4099.5342
43000 2.027217 0.053657298 2.0786218 0.79779536 4050.1962
44000 2.0107551 0.07427185 2.0827928 0.88949517 4022.2995
45000 2.035579 0.054511708 2.087829 0.85058092 3982.0592
46000 1.9855666 0.1079948 2.0913552 0.96268676 3937.279
47000 1.9938397 0.095380271 2.0870046 0.94036115 3882.9266
48000 2.0056151 0.087885527 2.0912722 0.94935203 3824.2309
49000 2.0079615 0.089440768 2.0951712 0.97596247 3781.8079
50000 1.9875181 0.10628651 2.0915963 1.1315334 3749.1501
Loop time of 8.39356 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 4.0534 (48.2918)
Neigh time (%) = 1.32911 (15.8349)
Comm time (%) = 0.318698 (3.79693)
Outpt time (%) = 0.000521898 (0.00621784)
Other time (%) = 2.69183 (32.0702)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 548 ave 548 max 548 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6073 ave 6073 max 6073 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6073
Ave neighs/atom = 6.74778
Neighbor list builds = 3122
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

135
examples/colloid/log.15May15.colloid.g++.4 Normal file
View File

@ -0,0 +1,135 @@
LAMMPS (30 Apr 2015)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
comm_modify mode multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 13.5
Memory usage per processor = 3.76692 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011
2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014
3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78
4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579
5000 2.1407629 0.016107891 2.1544922 0.076141723 28576.1
6000 2.1131348 0.00051000844 2.1112968 0.095061489 21598.174
7000 2.0735911 0.011894403 2.0831815 0.11729552 17864.933
8000 2.0619661 0.0060168177 2.0656919 0.1295732 15547.781
9000 2.0595354 0.0024157411 2.0596627 0.14657861 13836.694
10000 2.0425447 0.018278949 2.0585541 0.1740235 12474.354
11000 2.0460068 0.012079252 2.0558127 0.19227728 11392.874
12000 2.0372027 0.019110617 2.0540498 0.21648482 10523.896
13000 2.0416804 0.015790699 2.0552026 0.24604625 9785.1314
14000 2.0466943 0.0064454505 2.0508656 0.22777839 9165.8411
15000 2.0436536 0.015576669 2.0569595 0.28266826 8582.5053
16000 2.0335541 0.01998798 2.0512825 0.2894612 8114.5044
17000 2.0109406 0.039132968 2.0478392 0.34665262 7758.9312
18000 2.016964 0.038362354 2.0530852 0.37108874 7399.6774
19000 2.0399584 0.012731426 2.0504232 0.32979629 7081.8066
20000 2.0260154 0.027880228 2.0516445 0.36371005 6812.6037
21000 2.0321966 0.023814364 2.053753 0.36376888 6556.4552
22000 1.9850947 0.072749763 2.0556388 0.52542507 6293.5003
23000 2.0360536 0.02395391 2.0577452 0.42540507 6061.6557
24000 2.0237181 0.032711377 2.0541809 0.43998497 5883.2886
25000 2.0145711 0.042376354 2.0547091 0.54706192 5715.4423
26000 2.00533 0.049986982 2.0530888 0.55453953 5564.0132
27000 2.0266398 0.035044901 2.0594329 0.51842026 5431.0259
28000 2.0321757 0.029913711 2.0598314 0.49663872 5305.2909
29000 1.9964359 0.066498777 2.0607164 0.56461185 5174.9947
30000 1.982908 0.082624709 2.0633294 0.65815484 5046.1903
31000 2.0141773 0.049027808 2.0609671 0.58512256 4980.1474
32000 1.9938427 0.076695158 2.0683225 0.64309333 4844.0907
33000 2.012869 0.054851302 2.0654838 0.63073652 4749.9868
34000 1.9867827 0.083467738 2.0680429 0.7840696 4656.3038
35000 2.0013706 0.067630614 2.0667775 0.72991936 4566.7052
36000 2.0106349 0.063148106 2.071549 0.73927159 4495.7351
37000 2.0245299 0.053399546 2.07568 0.7189467 4423.018
38000 2.0133929 0.062427506 2.0735833 0.74002573 4351.9277
39000 1.9874796 0.088021324 2.0732926 0.79349127 4293.1815
40000 2.0240342 0.057908137 2.0796935 0.75182186 4235.9306
41000 1.9973584 0.077969812 2.0731089 0.83868109 4218.8397
42000 2.0034131 0.079826384 2.0810134 0.78010078 4179.2254
43000 2.0438594 0.047617472 2.0892059 0.77402823 4089.0577
44000 2.021871 0.066506327 2.0861308 0.82593265 3999.9932
45000 2.0052391 0.07876379 2.0817748 0.84100298 3958.8163
46000 2.0163501 0.073621087 2.0877308 0.8621767 3920.4982
47000 2.020619 0.067706551 2.0860804 0.92651509 3885.827
48000 2.0168306 0.082111421 2.0967011 0.9214563 3829.1155
49000 2.0007804 0.098241181 2.0967985 0.93140657 3755.3901
50000 2.0213773 0.071280328 2.0904116 0.9408025 3734.5105
Loop time of 3.45766 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.04423 (30.2006)
Neigh time (%) = 0.340227 (9.8398)
Comm time (%) = 0.816549 (23.6156)
Outpt time (%) = 0.000828743 (0.0239683)
Other time (%) = 1.25582 (36.32)
Nlocal: 225 ave 234 max 208 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 305.25 ave 313 max 299 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 1501.75 ave 1627 max 1408 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 6007
Ave neighs/atom = 6.67444
Neighbor list builds = 3071
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation