Hi,
I tried to play with the values of neighbor skin on my simulation. Simulation method is DPD, the system is 2%-5% linear surfactant in water at density equals to 3, and the condition is at room temperature.
My question is about the neighbor. I used the safest setting that “delay 0 every 1 check yes,” and time step is small enough that the nve only has <0.01 temperature fluctuation (lj unit). I gradually increased the neighbor skin starting from 0.0 bin. While the skin reached to 0.3 bin (default in lj unit), the warning for dangerous build became zero. However, I tried a even longer neighbor distance 2 bin, and the thermo outputs are not identical to those in 0.3 bin (very close though, see below). The simulation takes long, so I am not sure whether the final system configuration will be the same for both case (0.3 & 2). I want to save CPU time, but I just want to confirm that using 0.3 bin is completely safe in this scenario. Thank you.
=====For 0.3 bin===========
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 15.3038 KinEng = 0.0000 Temp = 0.0000
PotEng = 15.3038 E_bond = 0.0029 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 15.3009
E_coul = 0.0000 E_long = 0.0000 Press = 95.0297
---------------- Step 1000 ----- CPU = 40.5580 (sec) ----------------
TotEng = 17.8743 KinEng = 1.5099 Temp = 1.0066
PotEng = 16.3644 E_bond = 0.0474 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3170
E_coul = 0.0000 E_long = 0.0000 Press = 93.9090
---------------- Step 2000 ----- CPU = 83.0964 (sec) ----------------
TotEng = 17.8606 KinEng = 1.5068 Temp = 1.0045
PotEng = 16.3538 E_bond = 0.0517 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3020
E_coul = 0.0000 E_long = 0.0000 Press = 93.9462
---------------- Step 3000 ----- CPU = 125.6529 (sec) ----------------
TotEng = 17.8761 KinEng = 1.5145 Temp = 1.0097
PotEng = 16.3617 E_bond = 0.0518 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3099
E_coul = 0.0000 E_long = 0.0000 Press = 93.8502
---------------- Step 4000 ----- CPU = 168.0624 (sec) ----------------
TotEng = 17.8723 KinEng = 1.5168 Temp = 1.0112
PotEng = 16.3554 E_bond = 0.0526 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3028
E_coul = 0.0000 E_long = 0.0000 Press = 93.9326
---------------- Step 5000 ----- CPU = 210.8077 (sec) ----------------
TotEng = 17.8825 KinEng = 1.5221 Temp = 1.0148
PotEng = 16.3604 E_bond = 0.0527 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3077
E_coul = 0.0000 E_long = 0.0000 Press = 93.8698
Loop time of 210.807 on 8 procs for 5000 steps with 81000 atoms
Pair time () = 96.7146 (45.8783)
Bond time () = 0.145177 (0.0688672)
Neigh time () = 57.6921 (27.3673)
Comm time () = 46.4736 (22.0456)
Outpt time () = 0.0418394 (0.0198472)
Other time () = 9.73963 (4.62017)
Nlocal: 10125 ave 10158 max 10095 min
Histogram: 2 0 0 2 1 0 0 1 0 2
Nghost: 6230.62 ave 6268 max 6179 min
Histogram: 1 0 1 0 1 0 2 1 1 1
Neighs: 129504 ave 130240 max 128810 min
Histogram: 1 0 2 2 0 0 0 1 0 2
Total # of neighbors = 1036030
Ave neighs/atom = 12.7905
Ave special neighs/atom = 0.08
Neighbor list builds = 2498
Dangerous builds = 0
=========For 2 bin============================
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 15.3038 KinEng = 0.0000 Temp = 0.0000
PotEng = 15.3038 E_bond = 0.0029 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 15.3009
E_coul = 0.0000 E_long = 0.0000 Press = 95.0296
---------------- Step 1000 ----- CPU = 84.2002 (sec) ----------------
TotEng = 17.8801 KinEng = 1.5180 Temp = 1.0120
PotEng = 16.3620 E_bond = 0.0471 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3149
E_coul = 0.0000 E_long = 0.0000 Press = 93.9302
---------------- Step 2000 ----- CPU = 177.4987 (sec) ----------------
TotEng = 17.8768 KinEng = 1.5161 Temp = 1.0108
PotEng = 16.3607 E_bond = 0.0505 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3102
E_coul = 0.0000 E_long = 0.0000 Press = 93.8860
---------------- Step 3000 ----- CPU = 271.2379 (sec) ----------------
TotEng = 17.8745 KinEng = 1.5194 Temp = 1.0130
PotEng = 16.3550 E_bond = 0.0519 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3032
E_coul = 0.0000 E_long = 0.0000 Press = 93.9626
---------------- Step 4000 ----- CPU = 364.3931 (sec) ----------------
TotEng = 17.8705 KinEng = 1.5138 Temp = 1.0092
PotEng = 16.3566 E_bond = 0.0500 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3066
E_coul = 0.0000 E_long = 0.0000 Press = 93.8757
---------------- Step 5000 ----- CPU = 457.6378 (sec) ----------------
TotEng = 17.8738 KinEng = 1.5135 Temp = 1.0090
PotEng = 16.3604 E_bond = 0.0519 E_angle = 0.0000
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = 16.3085
E_coul = 0.0000 E_long = 0.0000 Press = 93.8567
Loop time of 457.642 on 8 procs for 5000 steps with 81000 atoms
Pair time () = 302.299 (66.0556)
Bond time () = 0.164744 (0.0359984)
Neigh time () = 64.1674 (14.0213)
Comm time () = 79.734 (17.4228)
Outpt time () = 0.0432346 (0.00944726)
Other time () = 11.2344 (2.45484)
Nlocal: 10125 ave 10145 max 10099 min
Histogram: 1 0 1 1 1 0 0 1 1 2
Nghost: 17617.1 ave 17660 max 17565 min
Histogram: 1 0 0 1 1 2 1 0 1 1
Neighs: 1.71306e+06 ave 1.71979e+06 max 1.70526e+06 min
Histogram: 1 0 0 1 1 2 1 1 0 1
Total # of neighbors = 13704495
Ave neighs/atom = 169.191
Ave special neighs/atom = 0.08
Neighbor list builds = 361
Dangerous builds = 0