Hello All,
I have been trying to simulate Adsorption of N2 in IRMOF-1. I have built a model for equilibration of the simulation, and I am not able to run the minimization, I tried running it using fix langevin and fix nve as suggested in moltemplate, I also tried minimization using cg, sd, fire, quickmin. I have tried increasing the cutoff distance, reducing the neighbor skin distance, reducing the timestep but I still keep getting the same error. It maybe because the traPPE model of N2 I’m using, but I’m not sure and I haven’t found any other model for N2 to verify this as well. Can someone please take a look and help me find the error?
Thank you!
data.IRMOF-1.lammps (171.3 KB)
n2.mol.lammps (474 Bytes)
in.EQUI.lammps.step1 (4.2 KB)
The only logical explanation would be that your force field parameters are not suitable.
Your initial geometry has very high potential energy due to a close contact.
running a minimization should help to eliminate this, and for a bit it looks like it works, but then things go bad and then worse. If you would create a dump file of the minimization steps you should see how the system starts to disintegrate and you can from it identify which atoms/bonds/interactions don’t work well.
Unit style : real
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 22.81 | 22.81 | 22.81 Mbytes
Step Temp E_pair E_mol TotEng Press
0 77 3.4486896e+14 132723.31 3.4486896e+14 5.4241312e+15
1 77 9.8547958e+13 132725.37 9.8547959e+13 1.5499715e+15
2 77 2.3187615e+13 132727.31 2.3187615e+13 3.6469701e+14
3 77 8.2527239e+12 132729.5 8.252724e+12 1.2979964e+14
4 77 1.7986224e+12 132740.06 1.7986225e+12 2.8288919e+13
5 77 5.7273747e+11 132762.99 5.727376e+11 9.0080801e+12
6 77 1.5234517e+11 132774.23 1.5234531e+11 2.3961064e+12
7 77 4.6598027e+10 132789.09 4.659816e+10 7.3290308e+11
8 77 7.1274861e+09 132785.92 7.1276192e+09 1.1210459e+11
9 77 2.8217191e+09 132731.08 2.8218521e+09 4.4382445e+10
10 77 1.1011216e+09 132652.88 1.1012545e+09 1.732018e+10
11 77 3.6055529e+08 132536.17 3.6068808e+08 5.6720071e+09
12 77 1.9233799e+08 132565.27 1.9247081e+08 3.0260661e+09
13 77 1.2415646e+08 132618.93 1.2428933e+08 1.9535951e+09
14 77 44102626 132919.71 44235799 6.9428664e+08
15 77 18876127 133367.79 19009748 2.9739565e+08
16 77 8482501.3 134050.31 8616804.3 1.3383224e+08
17 77 5911071.3 134412.18 6045736.2 93355693
18 77 3087717.3 135296.16 3223266.2 48897216
19 77 1870232.9 136032.2 2006517.8 29714534
20 77 1101896.4 137078.54 1239227.6 17598571
21 77 677934.73 138094.12 816281.55 10904550
22 77 412992.22 139317.76 552562.68 6712939.1
23 77 267175.09 140248.32 407676.11 4399549.1
24 77 181392.73 140753.53 322398.97 3033951.4
25 77 125106.79 140395.73 265755.22 2134814.2
26 77 93570.996 138960.8 232784.5 1630257.5
27 77 69717.445 135849.86 205820.01 1248986.7
28 77 54434.119 131021.42 185708.24 1006664
29 77 42280.891 123602.93 166136.53 816448.24
30 77 34177.029 114445.01 148874.74 692472.21
31 77 28773.087 104878.32 133904.11 611335.91
32 77 26451.393 99703.543 126407.64 576791.09
33 77 23971.591 92764.559 116988.85 540143.85
34 77 22278.115 87695.806 110226.63 514747.14
35 77 20023.793 79399.272 99675.77 480562.03
36 77 18726.787 74412.357 93391.849 460216.32
37 77 17149.915 67378.778 84781.397 434677.32
38 77 15876.812 61415.001 77544.518 413042.47
39 77 14662.545 55395.275 70310.524 391394.63
40 77 13503.09 49493.552 63249.346 369675.03
41 77 12513.731 44510.938 57277.373 350375.94
42 77 11629.162 40209.187 52091.054 332654.19
43 77 10775.47 36302.252 47330.426 315342.79
44 77 9895.0567 32664.127 42811.888 297861.3
45 77 9006.4005 29925.162 39184.267 283471.49
46 77 2981.6805 29048.379 32282.764 271196.95
47 77 -2829.904 28942.881 26365.681 263041.08
48 77 -19445.647 28941.625 9748.682 241248.88
49 77 -174787.83 28941.915 -145593.21 37649.303
50 77 -510965.92 28941.988 -481771.23 -402969.84
51 77 -12007057 28941.97 -11977862 -15470602
52 77 -31513880 28941.969 -31484685 -41037696
53 77 -3.3477647e+08 28941.969 -3.3474727e+08 -4.385162e+08
54 77 -1.6529247e+09 28941.969 -1.6528955e+09 -2.1661793e+09
55 77 -3.4128705e+09 28941.969 -3.4128413e+09 -4.4728948e+09
56 77 -6.4107161e+09 28941.969 -6.4106869e+09 -8.402102e+09
57 77 -1.4596497e+10 28941.969 -1.4596468e+10 -1.9130969e+10
58 77 -8.0742993e+10 28941.969 -8.0742964e+10 -1.0582758e+11
59 77 -6.0747408e+11 28941.969 -6.0747405e+11 -7.9620124e+11
60 77 -9.2816768e+12 28941.969 -9.2816768e+12 -1.2165805e+13
61 77 -5.2556258e+14 28941.969 -5.2556258e+14 -6.8812608e+14
62 77 -4.8433094e+15 28941.969 -4.8433094e+15 -6.6405968e+15
63 77 -6.1263557e+16 28941.969 -6.1263557e+16 294653.87
64 77 -3.0631778e+16 28941.969 -3.0631778e+16 -4.7222022e+16
Hi Alex!
Thanks for your reply. Yes, I came to the same conclusion. Now I have to sit and check the forcefield and the dump file. It’s going to be a long night 
Hello all,
- As @akohlmey suggested earlier, I created a dump file and have found out that, there is a problem with my model of N2, I have tried a couple of different models since with a ghost molecule for a quadruple in N2 molecule, but with mass of ghost atom set to 1e-20 (for 0 approximation) it keeps giving error, but if I assign some mass to it (which is obviously incorrect) my simulation runs well. Now, as far as I understand this is because with finite mass, the acceleration of the molecule keeps in check and the velocities are finite. So my question is, can we describe the quadruple to lammps without using a ghost atom?
- One more problem is, as I am creating molecules in the simulation cell using ‘create_atom random’ there are many overlaps and I have to run minimization to reduce the overlaps, but as written in the documentation, I can’t use fix rigid for the N2 molecules and the molecule becomes flexible (N-ghost-N angle changes from 180degress significantly for majority of molecules). So is there a work around for this, maybe minimizing using fix viscous or fix langevin? (I tried both of them, but it keeps giving the bond atoms missing error).
No, or at least not without changing a significant amount of source code. The best way to handle this case with the existing code would be to use fix rigid/small for time integration of that molecule. Then the small mass does not matter, because the limitations on the timestep com from the total mass and the moments of inertia, since fix rigid/small does time integration of the center of mass and the orientation of the entire rigid object.
You could try doing the insertions via fix gcmc. See examples/mc/in.gcmc.co2.
With fix gcmc only insertions that do not create too high a rise in energy are accepted.