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标题: 求助：lammps跑CO2和H2O输出轨迹文件中CO2的C=O键过长。若是力场原因是否有合适力场 [打印本页]

作者
Author: 25110031 时间: 2023-4-24 20:41
标题: 求助：lammps跑CO2和H2O输出轨迹文件中CO2的C=O键过长。若是力场原因是否有合适力场
本帖最后由 25110031 于 2023-4-25 09:26 编辑

小弟在做碳化对钝化膜的影响，但是h2o和c2o混合后的模型中co2键长一跑就变成图片中那样，是VMD设置问题、模型还是力场文件的问题，希望能有大神指点一番，最近刚刚接触lammps。

这是VMD查看的轨迹文件

(, 下载次数 Times of downloads: 14)
data文件：960 atoms
3 atom types
0.0 23.22 xlo xhi
0.0 100.0 ylo yhi
0.0 21.42 zlo zhi
Masses

1 15.9990 #O
2 1.0080 #H
3 12.0000 #C

Atoms  # charge

力场文件

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
0.0000 !not used
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

in文件
# REAX potential for CHO system
# .....

units             real

atom_style       charge
atom_modify map yes
read_data       sys.data

pair_style       reax/c lmp_control
pair_coeff       * * reaxff_C_H_O O H C

neighbor       2 bin
neigh_modify       every 10 delay 0 check no

#group feooh id 1:1003
#group fluid id 1004:2878

#fix 11 fluid addforce 0.0 0.0 0.0
#fix 12 feooh setforce 0.0 0.0 0.0

fix             1 all nve
fix          2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
fix          3 all temp/berendsen 298.0 298.0 100.0

timestep       0.25

dump             1 all custom 1000 dump.lammpstrj id type x y z ix iy iz
dump_modify       1 sort id
thermo 100
thermo_style custom step cpu temp press etotal

run             1000000
轨迹文件 (, 下载次数 Times of downloads: 1)

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