forked from lijiext/lammps
165 lines
9.0 KiB
Groff
165 lines
9.0 KiB
Groff
LAMMPS (29 Sep 2021)
|
|
# test script for fix mol/swap
|
|
# initial system is 50/50 chains of type 1 and type 2
|
|
# b/c epsilon12 is set to 1.02 (weakly same as 1/1 or 1/2) the
|
|
# system will stay in equilibrium as a mix of both chain types
|
|
# fix mol/swap helps this happen quickly
|
|
# see the last 2 columns of thermo output for counts of 2 chain types
|
|
|
|
units lj
|
|
atom_style angle
|
|
neighbor 0.36 bin
|
|
neigh_modify delay 0
|
|
|
|
pair_style lj/cut 1.1224620483
|
|
bond_style fene
|
|
angle_style cosine
|
|
special_bonds lj 0.0 1.0 1.0
|
|
|
|
read_data data.bead
|
|
Reading data file ...
|
|
orthogonal box = (-8.2115700 -8.2115700 -8.2115700) to (8.2115700 8.2115700 8.2115700)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
4000 atoms
|
|
scanning bonds ...
|
|
1 = max bonds/atom
|
|
scanning angles ...
|
|
1 = max angles/atom
|
|
reading bonds ...
|
|
3900 bonds
|
|
reading angles ...
|
|
3800 angles
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 1 1
|
|
special bond factors coul: 0 0 0
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of 1-3 neighbors
|
|
4 = max # of 1-4 neighbors
|
|
6 = max # of special neighbors
|
|
special bonds CPU = 0.001 seconds
|
|
read_data CPU = 0.028 seconds
|
|
|
|
pair_coeff * * 1.0 1.0 1.1224620483
|
|
pair_coeff 1 2 1.02 1.0 1.1224620483
|
|
bond_coeff 1 30.0 1.5 1.0 1.0
|
|
angle_coeff 1 1.500
|
|
pair_modify shift yes
|
|
|
|
variable vt1 atom type==1
|
|
variable vt2 atom type==2
|
|
group g1 dynamic all var vt1 every 100
|
|
dynamic group g1 defined
|
|
group g2 dynamic all var vt2 every 100
|
|
dynamic group g2 defined
|
|
variable count1 equal count(g1)
|
|
variable count2 equal count(g2)
|
|
|
|
timestep 0.010
|
|
|
|
fix 1 all langevin 1.0 1.0 100.0 702547
|
|
fix 2 all nve
|
|
fix 3 all mol/swap 100 1 1 2 482794 1.0
|
|
|
|
compute p all pressure thermo_temp
|
|
thermo 1000
|
|
thermo_style custom step temp etotal press f_3[1] f_3[2] v_count1 v_count2
|
|
|
|
run 50000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 1.482462
|
|
ghost atom cutoff = 1.482462
|
|
binsize = 0.74123102, bins = 23 23 23
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
WARNING: Communication cutoff 1.4824620483 is shorter than a bond length based estimate of 1.815. This may lead to errors. (../comm.cpp:728)
|
|
Per MPI rank memory allocation (min/avg/max) = 5.313 | 5.314 | 5.314 Mbytes
|
|
Step Temp TotEng Press f_3[1] f_3[2] v_count1 v_count2
|
|
0 0 21.451627 5.079399 0 0 2000 2000
|
|
1000 0.49011138 21.59359 4.2337989 10 10 2000 2000
|
|
2000 0.55288866 21.724374 4.4596786 20 20 2080 1920
|
|
3000 0.59299724 21.844178 4.6112243 30 29 2280 1720
|
|
4000 0.64746348 21.964318 4.9463669 40 39 2280 1720
|
|
5000 0.67853936 22.053147 5.1950218 50 48 2320 1680
|
|
6000 0.70751144 22.147453 5.0636869 60 58 2240 1760
|
|
7000 0.73570064 22.233705 5.4872622 70 68 2160 1840
|
|
8000 0.7677554 22.312938 5.4283736 80 77 2360 1640
|
|
9000 0.78493237 22.383155 5.8547233 90 87 2440 1560
|
|
10000 0.80634514 22.449402 5.8785731 100 96 2400 1600
|
|
11000 0.82563194 22.475286 5.8193738 110 104 2400 1600
|
|
12000 0.81684024 22.527492 6.0323967 120 114 2320 1680
|
|
13000 0.84497155 22.567888 6.0488755 130 122 2240 1760
|
|
14000 0.85452242 22.606908 6.1983634 140 132 2080 1920
|
|
15000 0.88109242 22.654336 6.1408279 150 141 1960 2040
|
|
16000 0.88925915 22.707597 6.1560975 160 150 2000 2000
|
|
17000 0.91598439 22.762791 6.1071728 170 160 2000 2000
|
|
18000 0.92453211 22.778304 6.3330693 180 170 2240 1760
|
|
19000 0.92839551 22.797316 6.2917909 190 180 2000 2000
|
|
20000 0.93054033 22.819289 6.091701 200 189 2200 1800
|
|
21000 0.93955351 22.844135 6.5833013 210 198 2000 2000
|
|
22000 0.94454858 22.856272 6.5661753 220 207 2200 1800
|
|
23000 0.95446407 22.878735 6.5957294 230 216 2160 1840
|
|
24000 0.94748257 22.894539 6.6187447 240 226 1920 2080
|
|
25000 0.95732202 22.912292 6.4795471 250 236 1680 2320
|
|
26000 0.96970172 22.908988 6.537366 260 245 1720 2280
|
|
27000 0.96032166 22.924899 6.6238248 270 255 1960 2040
|
|
28000 0.96197769 22.9358 6.8926097 280 264 1920 2080
|
|
29000 0.98745595 22.964694 6.5839025 290 271 2040 1960
|
|
30000 0.99264869 22.947884 6.3893499 300 280 1920 2080
|
|
31000 0.96953069 22.957927 6.6616047 310 289 1800 2200
|
|
32000 0.99955117 22.963979 6.5958456 320 298 1680 2320
|
|
33000 0.97090103 22.969029 6.9087296 330 307 1800 2200
|
|
34000 0.99818457 22.988477 6.6471994 340 316 1920 2080
|
|
35000 0.9965288 22.992883 6.9691785 350 325 2040 1960
|
|
36000 0.99533174 22.983774 6.6585089 360 334 2000 2000
|
|
37000 0.98819278 22.995387 6.618802 370 344 2080 1920
|
|
38000 0.99598576 22.991892 6.7536669 380 354 2080 1920
|
|
39000 0.99312702 22.989239 6.4028165 390 364 2080 1920
|
|
40000 1.0035821 23.001944 6.9307671 400 374 1920 2080
|
|
41000 0.99914733 23.00134 6.6251677 410 383 1880 2120
|
|
42000 0.98054536 22.981781 6.5918554 420 393 1880 2120
|
|
43000 0.99413829 23.008 6.7390795 430 403 1720 2280
|
|
44000 0.98867961 23.00521 6.8505543 440 412 1600 2400
|
|
45000 0.99626811 23.019995 6.827741 450 421 1640 2360
|
|
46000 1.0186043 23.020759 6.6195562 460 430 1680 2320
|
|
47000 1.0121335 23.019271 6.6022102 470 439 1800 2200
|
|
48000 0.99883756 23.013973 6.5255522 480 448 1920 2080
|
|
49000 0.99425223 23.022708 6.609746 490 458 2240 1760
|
|
50000 0.99505489 23.012641 6.4592863 500 468 2240 1760
|
|
Loop time of 19.4175 on 4 procs for 50000 steps with 4000 atoms
|
|
|
|
Performance: 2224796.830 tau/day, 2574.996 timesteps/s
|
|
95.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 2.5467 | 2.6684 | 2.7896 | 6.3 | 13.74
|
|
Bond | 2.3037 | 2.4117 | 2.5085 | 5.3 | 12.42
|
|
Neigh | 7.3597 | 7.3633 | 7.3673 | 0.1 | 37.92
|
|
Comm | 3.0482 | 3.2694 | 3.4997 | 10.2 | 16.84
|
|
Output | 0.0014609 | 0.0017069 | 0.0021793 | 0.7 | 0.01
|
|
Modify | 2.9624 | 3.0581 | 3.1424 | 4.7 | 15.75
|
|
Other | | 0.6447 | | | 3.32
|
|
|
|
Nlocal: 1000.00 ave 1013 max 986 min
|
|
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
Nghost: 1186.25 ave 1198 max 1178 min
|
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
|
Neighs: 4927.00 ave 5028 max 4790 min
|
|
Histogram: 1 0 0 0 0 1 0 1 0 1
|
|
|
|
Total # of neighbors = 19708
|
|
Ave neighs/atom = 4.9270000
|
|
Ave special neighs/atom = 5.7000000
|
|
Neighbor list builds = 10721
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:19
|