Hi All,
I tested my reax simulation by using lammps-stable-29Sep21, there are something wrong:
-
ERROR: Lost atoms: original 105 current 104, when some reaction happens and make some new molecule.
It is still for adding minimize or changing other temperature control, did I missing some parameters or method? -
ERROR: Illegal fix ave/atom command, when Nevery >=1000 in ‘fix reaxff/species’ command
Is there some limits in fix ave/atom or fix reaxff/species? but Nevery >= 1000 is legal in ‘fix reaxff/bonds’
File are here (new user can not upload)
In file:
variable elements string ‘C C H O’
units real
atom_style charge
read_data reax.data
pair_style reaxff lmp_control
pair_coeff * * CHO_test.reax {elements}
fix q all qeq/reaxff 1 0.0 10.0 1e-6 reaxff
neighbor 2 bin
neigh_modify every 10 delay 0 check yes
variable timestep equal 1
variable Tstart equal 1000
variable Tstop equal 1000
variable Tdamp equal 100
variable Nthermo equal 500
variable Ndump equal 500
variable Ntotal equal 5000
reset_timestep 0
#minimize 1.0e-6 1.0e-6 1000 1000
#reset_timestep 0
velocity all create {Tstart} 123456
timestep {timestep}
fix 1 all nve
fix 4 all temp/rescale 500 {Tstart} {Tstop} 0.02 0.5
fix r1 all reaxff/species {Nthermo} 1 {Nthermo} species1.out element {elements}
fix r2 all reaxff/bonds {Nthermo} bonds.reaxff
thermo {Nthermo}
thermo_style custom step temp
run ${Ntotal}
Data file:
#LAMMPS data file
105 atoms
4 atom types
4.8145 32.1263 xlo xhi
-3.4089 25.1135 ylo yhi
-1.4579 24.8464 zlo zhi
0.0000 0.0000 0.0000 xy xz yz
Masses
1 12.0110 # C1
2 12.0110 # C2
3 1.0080 # H3
4 15.9994 # O4
Atoms # charge
1 2 -0.1800 13.3735 17.7444 19.9029 # C2
2 1 -0.1200 12.1668 18.6974 19.8199 # C1
3 1 -0.1200 12.6221 20.0452 19.2308 # C1
4 1 -0.1200 11.4194 21.0031 19.1448 # C1
5 2 -0.1800 11.8813 22.3486 18.5549 # C2
6 3 0.0600 13.0409 16.7448 20.3386 # H3
7 3 0.0600 14.1738 18.2035 20.5725 # H3
8 3 0.0600 13.8004 17.5808 18.8586 # H3
9 3 0.0600 11.7401 18.8635 20.8639 # H3
10 3 0.0600 11.3655 18.2407 19.1497 # H3
11 3 0.0600 13.0501 19.8785 18.1875 # H3
12 3 0.0600 13.4232 20.5012 19.9016 # H3
13 3 0.0600 10.9920 21.1711 20.1883 # H3
14 3 0.0600 10.6178 20.5475 18.4744 # H3
15 3 0.0600 12.6837 22.8018 19.2260 # H3
16 3 0.0600 10.9940 23.0614 18.4891 # H3
17 3 0.0600 12.3100 22.1785 17.5124 # H3
18 2 -0.1800 9.0771 2.4998 3.8603 # C2
19 1 -0.1200 9.3168 1.7735 2.5237 # C1
20 1 -0.1200 8.0189 1.7903 1.6954 # C1
21 1 -0.1200 8.2518 1.0654 0.3568 # C1
22 2 -0.1800 6.9507 1.0862 -0.4664 # C2
23 3 0.0600 10.0363 2.4890 4.4765 # H3
24 3 0.0600 8.2490 1.9695 4.4370 # H3
25 3 0.0600 8.7677 3.5780 3.6568 # H3
26 3 0.0600 9.6245 0.6947 2.7265 # H3
27 3 0.0600 10.1443 2.3029 1.9453 # H3
28 3 0.0600 7.7108 2.8693 1.4942 # H3
29 3 0.0600 7.1922 1.2608 2.2747 # H3
30 3 0.0600 8.5581 -0.0141 0.5573 # H3
31 3 0.0600 9.0784 1.5938 -0.2237 # H3
32 3 0.0600 6.1252 0.5576 0.1156 # H3
33 3 0.0600 7.1202 0.5499 -1.4579 # H3
34 3 0.0600 6.6437 2.1658 -0.6653 # H3
35 2 -0.1800 20.1192 19.9952 16.0051 # C2
36 1 -0.1200 20.8109 21.2398 16.5913 # C1
37 1 -0.1200 21.9463 20.7959 17.5323 # C1
38 1 -0.1200 22.6421 22.0364 18.1220 # C1
39 2 -0.1800 23.7763 21.5858 19.0615 # C2
40 3 0.0600 19.2777 20.3192 15.3078 # H3
41 3 0.0600 19.6895 19.3656 16.8527 # H3
42 3 0.0600 20.8800 19.3782 15.4219 # H3
43 3 0.0600 20.0519 21.8576 17.1761 # H3
44 3 0.0600 21.2429 21.8697 15.7450 # H3
45 3 0.0600 22.7049 20.1782 16.9470 # H3
46 3 0.0600 21.5145 20.1647 18.3776 # H3
47 3 0.0600 21.8848 22.6549 18.7082 # H3
48 3 0.0600 23.0752 22.6668 17.2766 # H3
49 3 0.0600 23.3411 20.9541 19.9048 # H3
50 3 0.0600 24.2941 22.5015 19.5009 # H3
51 3 0.0600 24.5320 20.9666 18.4741 # H3
52 2 -0.1800 9.8004 21.6934 11.4432 # C2
53 1 -0.1200 9.4849 20.3059 12.0320 # C1
54 1 -0.1200 10.7794 19.4748 12.0992 # C1
55 1 -0.1200 10.4709 18.0856 12.6873 # C1
56 2 -0.1800 11.7692 17.2599 12.7510 # C2
57 3 0.0600 8.8441 22.3118 11.3917 # H3
58 3 0.0600 10.2313 21.5710 10.3950 # H3
59 3 0.0600 10.5609 22.2236 12.1068 # H3
60 3 0.0600 8.7251 19.7744 11.3687 # H3
61 3 0.0600 9.0553 20.4261 13.0811 # H3
62 3 0.0600 11.5382 20.0080 12.7621 # H3
63 3 0.0600 11.2096 19.3556 11.0503 # H3
64 3 0.0600 9.7123 17.5518 12.0244 # H3
65 3 0.0600 10.0422 18.2035 13.7370 # H3
66 3 0.0600 12.1973 17.1439 11.7009 # H3
67 3 0.0600 11.5448 16.2302 13.1858 # H3
68 3 0.0600 12.5268 17.7957 13.4133 # H3
69 2 -0.1800 8.8893 11.7425 23.0852 # C2
70 1 -0.1200 8.8865 10.2062 23.1936 # C1
71 1 -0.1200 10.2832 9.6680 22.8323 # C1
72 1 -0.1200 10.2875 8.1318 22.9384 # C1
73 2 -0.1800 11.6866 7.6004 22.5758 # C2
74 3 0.0600 7.8571 12.1462 23.3517 # H3
75 3 0.0600 9.1528 12.0466 22.0186 # H3
76 3 0.0600 9.6626 12.1719 23.8044 # H3
77 3 0.0600 8.1148 9.7749 22.4738 # H3
78 3 0.0600 8.6252 9.8999 24.2601 # H3
79 3 0.0600 11.0546 10.1001 23.5519 # H3
80 3 0.0600 10.5449 9.9753 21.7662 # H3
81 3 0.0600 9.5170 7.6986 22.2185 # H3
82 3 0.0600 10.0272 7.8236 24.0046 # H3
83 3 0.0600 11.9459 7.9107 21.5100 # H3
84 3 0.0600 11.6936 6.4631 22.6532 # H3
85 3 0.0600 12.4562 8.0352 23.2957 # H3
86 4 0.0000 4.8145 17.9586 16.3995 # O4
87 4 0.0000 5.4527 17.7566 17.7190 # O4
88 4 0.0000 12.2686 8.6604 3.8234 # O4
89 4 0.0000 11.3721 9.7903 4.1555 # O4
90 4 0.0000 32.1263 -3.4089 5.3489 # O4
91 4 0.0000 30.7639 -3.2410 5.9022 # O4
92 4 0.0000 30.6491 19.5833 24.8464 # O4
93 4 0.0000 31.1059 19.4681 23.4436 # O4
94 4 0.0000 9.2394 16.2504 6.1390 # O4
95 4 0.0000 8.6784 15.7195 4.8766 # O4
96 4 0.0000 11.4891 19.7174 1.4015 # O4
97 4 0.0000 12.6875 19.0990 2.0107 # O4
98 4 0.0000 15.2709 25.1135 0.1081 # O4
99 4 0.0000 14.3401 24.3553 -0.7576 # O4
100 4 0.0000 29.0653 -0.8977 15.0760 # O4
101 4 0.0000 29.8570 -0.9440 16.3254 # O4
102 4 0.0000 8.3190 10.8988 16.8182 # O4
103 4 0.0000 8.0624 12.3411 16.6042 # O4
104 4 0.0000 26.8654 19.7593 11.3826 # O4
105 4 0.0000 25.7310 20.5925 11.8408 # O4
lmp_control:
tabulate_long_range 10000
nbrhood_cutoff 4.5
hbond_cutoff 6.0
bond_graph_cutoff 0.3
thb_cutoff 0.001
reax force field file:
Reactive MD-force field: c/h/o combustion force field November 2006
39 ! Number of general parameters
50.0000 !p(boc1)
9.5469 !p(boc2)
26.5405 !p(coa2)
1.5105 !p(trip4)
6.6630 !p(trip3)
0.0000 !kc2
1.0588 !p(ovun6)
4.6000 !p(trip2)
12.1176 !p(ovun7)
13.3056 !p(ovun8)
-70.1292 !p(trip1)
0.0000 !Lower Taper-radius (swa)
10.0000 !Upper Taper-radius (swb)
0.0000 !not used
33.8667 !p(val7)
6.0891 !p(lp1)
1.0563 !p(val9)
2.0384 !p(val10)
6.1431 !not used
6.9290 !p(pen2)
0.3989 !p(pen3)
3.9954 !p(pen4)
0.0000 !not used
5.7796 !p(tor2)
10.0000 !p(tor3)
1.9487 !p(tor4)
0.0000 !not used
2.1645 !p(cot2)
1.5591 !p(vdW1)
0.1000 !Cutoff for bond order*100 (cutoff)
2.1365 !p(coa4)
0.6991 !p(ovun4)
50.0000 !p(ovun3)
1.8512 !p(val8)
0.0000 !not used
0.0000 !not used
0.0000 !not used
1.0 !Version number
2.6962 !p(coa3)
3 ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma;ro(pi);Val(e)
alfa;gamma(w);Val(angle);p(ovun5);n.u.;chiEEM;etaEEM;n.u.
ro(pipi);p(lp2);Heat increment;p(boc4);p(boc3);p(boc5),n.u.;n.u.
p(ovun2);p(val3);n.u.;Val(boc);p(val5);n.u.;n.u.;n.u.
C 1.3825 4.0000 12.0000 1.9133 0.1853 0.9000 1.1359 4.0000
9.7602 2.1346 4.0000 33.2433 79.5548 5.8678 7.0000 0.0000
1.2104 0.0000 199.0303 8.6991 34.7289 13.3894 0.8563 0.0000
-2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000
H 0.7853 1.0000 1.0080 1.5904 0.0419 1.0206 -0.1000 1.0000
9.3557 5.0518 1.0000 0.0000 121.1250 5.3200 7.4366 1.0000
-0.1000 0.0000 62.4879 1.9771 3.3517 0.7571 1.0698 0.0000
-15.7683 2.1488 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
O 1.2477 2.0000 15.9990 1.9236 0.0904 1.0503 1.0863 6.0000
10.2127 7.7719 4.0000 36.9573 116.0768 8.5000 8.9989 2.0000
0.9088 1.0003 60.8726 20.4140 3.3754 0.2702 0.9745 0.0000
-3.6141 2.7025 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000
6 ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(bo5);13corr;n.u.;p(bo6),p(ovun1)
p(be2);p(bo3);p(bo4);n.u.;p(bo1);p(bo2)
1 1 156.5953 100.0397 80.0000 -0.8157 -0.4591 1.0000 37.7369 0.4235
0.4527 -0.1000 9.2605 1.0000 -0.0750 6.8316 1.0000 0.0000
1 2 170.2316 0.0000 0.0000 -0.5931 0.0000 1.0000 6.0000 0.7140
5.2267 1.0000 0.0000 1.0000 -0.0500 6.8315 0.0000 0.0000
2 2 156.0973 0.0000 0.0000 -0.1377 0.0000 1.0000 6.0000 0.8240
2.9907 1.0000 0.0000 1.0000 -0.0593 4.8358 0.0000 0.0000
1 3 160.4802 105.1693 23.3059 -0.3873 -0.1613 1.0000 10.8851 1.0000
0.5341 -0.3174 7.0303 1.0000 -0.1463 5.2913 0.0000 0.0000
3 3 60.1463 176.6202 51.1430 -0.2802 -0.1244 1.0000 29.6439 0.9114
0.2441 -0.1239 7.6487 1.0000 -0.1302 6.2919 1.0000 0.0000
2 3 180.4373 0.0000 0.0000 -0.8074 0.0000 1.0000 6.0000 0.5514
1.2490 1.0000 0.0000 1.0000 -0.0657 5.0451 0.0000 0.0000
3 ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);ro(pi);ro(pipi)
1 2 0.1219 1.4000 9.8442 1.1203 -1.0000 -1.0000
2 3 0.0344 1.6800 10.3247 0.9013 -1.0000 -1.0000
1 3 0.1131 1.8523 9.8442 1.2775 1.1342 1.0621
18 ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);p(val7);p(pen1);p(val4)
1 1 1 67.2326 22.0695 1.6286 0.0000 1.7959 15.4141 1.8089
1 1 2 65.2527 14.3185 6.2977 0.0000 0.5645 0.0000 1.1530
2 1 2 70.0840 25.3540 3.4508 0.0000 0.0050 0.0000 3.0000
1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
1 1 3 49.5561 7.3771 4.9568 0.0000 0.7533 15.9906 1.0010
3 1 3 77.1171 39.8746 2.5403 -24.3902 1.7740 -42.9758 2.1240
2 1 3 65.0000 14.2057 4.8649 0.0000 0.3504 0.0000 1.7185
1 3 1 74.3994 44.7500 0.7982 0.0000 3.0000 0.0000 1.0528
1 3 3 77.9854 36.6201 2.0201 0.0000 0.7434 67.0264 3.0000
3 3 3 80.7324 30.4554 0.9953 0.0000 1.6310 50.0000 1.0783
1 3 2 71.5018 21.7062 0.4735 0.0000 0.5186 0.0000 1.1793
2 3 3 84.9468 23.3540 1.5057 0.0000 2.6374 0.0000 1.3023
2 3 2 77.0645 10.4737 1.2895 0.0000 0.9924 0.0000 1.1043
1 2 3 0.0000 25.0000 3.0000 0.0000 1.0000 0.0000 1.0400
3 2 3 0.0000 0.0148 6.0000 0.0000 0.0000 0.0000 1.0400
2 2 3 0.0000 9.7025 6.0000 0.0000 0.0000 0.0000 1.0400
21 ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);n.u;n.u.
1 1 1 1 -0.2500 11.5822 0.1879 -4.7057 -2.2047 0.0000 0.0000
1 1 1 2 -0.2500 31.2596 0.1709 -4.6391 -1.9002 0.0000 0.0000
2 1 1 2 -0.1770 30.0252 0.4340 -5.0019 -2.0697 0.0000 0.0000
1 1 1 3 -0.7098 22.2951 0.0060 -2.5000 -2.1688 0.0000 0.0000
2 1 1 3 -0.3568 22.6472 0.6045 -4.0088 -1.0000 0.0000 0.0000
3 1 1 3 -0.0528 6.8150 0.7498 -5.0913 -1.0000 0.0000 0.0000
1 1 3 1 2.0007 25.5641 -0.0608 -2.6456 -1.1766 0.0000 0.0000
1 1 3 2 -1.1953 42.1545 -1.0000 -8.0821 -1.0000 0.0000 0.0000
2 1 3 1 -0.9284 34.3952 0.7285 -2.5440 -2.4641 0.0000 0.0000
2 1 3 2 -2.5000 79.6980 1.0000 -3.5697 -2.7501 0.0000 0.0000
1 1 3 3 -0.0179 5.0603 -0.1894 -2.5000 -2.0399 0.0000 0.0000
2 1 3 3 -0.5583 80.0000 1.0000 -4.4000 -3.0000 0.0000 0.0000
3 1 3 1 -2.5000 76.0427 -0.0141 -3.7586 -2.9000 0.0000 0.0000
3 1 3 2 0.0345 78.9586 -0.6810 -4.1777 -3.0000 0.0000 0.0000
3 1 3 3 -2.5000 66.3525 0.3986 -3.0293 -3.0000 0.0000 0.0000
1 3 3 1 2.5000 -0.5332 1.0000 -3.5096 -2.9000 0.0000 0.0000
1 3 3 2 -2.5000 3.3219 0.7180 -5.2021 -2.9330 0.0000 0.0000
2 3 3 2 2.2500 -6.2288 1.0000 -2.6189 -1.0000 0.0000 0.0000
1 3 3 3 0.0531 -17.3983 1.0000 -2.5000 -2.1584 0.0000 0.0000
2 3 3 3 0.4723 -12.4144 -1.0000 -2.5000 -1.0000 0.0000 0.0000
3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -1.0000 0.0000 0.0000
0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000
0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
1 ! Nr of hydrogen bonds. at1;at2;at3;r(hb);p(hb1);p(hb2);p(hb3)
3 2 3 1.9682 -4.4628 1.7976 3.0000
Thanks!
Friz