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标题: MS聚合物建模，导出的元素类型增多。反应力场不兼容了 [打印本页]

作者
Author: 456321789 时间: 2023-8-29 20:25
标题: MS聚合物建模，导出的元素类型增多。反应力场不兼容了
大佬们，我用Lammps跑反应力场时遇见了一个棘手问题，非常的鸡肋。
我用Materials Studio建立了聚酰亚胺聚合物的模型，模型由CHON四种元素组成。然后，当使用了Lammps插件将其转换为Lammps可读的data时，出现了9种元素。
这导致我的聚合物反应力场中的C、H、O、N四种元素与模型data文件不兼容了。
部分主要模型数据如下：
LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 / CGCMM for 0.8

1230 atoms
1350 bonds
2190 angles
3360 dihedrals
720 impropers

9 atom types
  11 bond types
  19 angle types
  30 dihedral types
9 improper types

-0.629325101 28.188974899 xlo xhi
-0.574393600 28.243906400 ylo yhi
-0.846479539 27.971820461 zlo zhi

Masses

1  12.011150 # cp
2  15.999400 # oc
3  12.011150 # c5
4  12.011150 # c_1
5  14.010000 # n_2
6  14.006700 # nb
7  15.999400 # o_1
8 1.007970 # hc
9 1.008000 # hn2

Pair Coeffs # lj/class2/coul/long

1 0.0640000000 4.0100000000 # cp
2 0.2400000000 3.5350000000 # oc
3 0.0640000000 4.0100000000 # c5
4 0.1200000000 3.8100000000 # c_1
5 0.1060000000 3.6000000000 # n_2
6 0.0650000000 4.0700000000 # nb
7 0.2670000000 3.3000000000 # o_1
8 0.0200000000 2.9950000000 # hc
9 0.0130000000 1.6500000000 # hn2

Bond Coeffs # class2

1    1.4170 470.8361  -627.6179  1327.6345 # cp-cp
2    1.3912 447.0438  -784.5346 886.1671 # cp-nb
3    1.0982 372.8251  -803.4526 894.3173 # cp-hc
4    1.3768 428.8798  -738.2351  1114.9655 # cp-oc
5    1.4170 470.8361  -627.6179  1327.6345 # c5-c5
6    1.4170 470.8361  -627.6179  1327.6345 # cp-c5
7    1.4890 339.3574  -655.7236 670.2362 # c5-c_1
8    1.3660 390.6783  -768.3798 923.2418 # c_1-n_2
9    1.2020 851.1403 -1918.4882  2160.7659 # c_1-o_1
  10    0.0000    0.0000    0.0000    0.0000 # c_1-nb
  11    0.9959 495.8294 -1092.7239  1441.1290 # n_2-hn2

Angle Coeffs # class2

1 118.9000 61.0226 -34.9931    0.0000 # cp-cp-cp
2 121.4584 61.0647 -21.6172    0.0000 # cp-cp-nb
3 117.9400 35.1558 -12.4682    0.0000 # cp-cp-hc
4 123.4200 73.6781 -21.6787    0.0000 # cp-cp-oc
5    0.0000    0.0000    0.0000    0.0000 # cp-oc-cp
6 118.9000 61.0226 -34.9931    0.0000 # cp-c5-c5
7 116.0640 71.2598 -15.8273    2.0506 # c5-c5-c_1
8 116.0640 71.2598 -15.8273    2.0506 # cp-c5-c_1
9 118.9000 61.0226 -34.9931    0.0000 # c5-cp-c5
  10 117.9400 35.1558 -12.4682    0.0000 # c5-cp-hc
  11 108.4400 84.8377 -19.9640    2.7405 # c5-c_1-n_2
  12 125.5320 72.3167 -16.0650    2.0818 # c5-c_1-o_1
  13 125.5320 101.8765 -41.8094    0.0000 # n_2-c_1-o_1
  14    0.0000    0.0000    0.0000    0.0000 # c5-c_1-nb
  15    0.0000    0.0000    0.0000    0.0000 # nb-c_1-o_1
  16    0.0000    0.0000    0.0000    0.0000 # c_1-n_2-c_1
  17 122.9480 40.4820 -16.2028    0.0000 # c_1-n_2-hn2
  18    0.0000    0.0000    0.0000    0.0000 # c_1-nb-c_1
  19    0.0000    0.0000    0.0000    0.0000 # cp-nb-c_1
......

力场文件如下：
Reactive MD-force field: Combustion C/H/O force field + atom type N (May11, 2018)
40 ! Number of general parameters
50.0000 !p(boc1)
9.5469 !p(boc2)
26.5405 !p(coa2)
0.6863 !p(trip4)
2.7295 !p(trip3)
70.0000 !kc2
1.0588 !p(ovun6)
4.1262 !p(trip2)
12.1176 !p(ovun7)
13.3056 !p(ovun8)
-68.9784 !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
1.0000 !not used
2.6962 !p(coa3)
2.0000 !triple bond on/off (0 for CO, 1 for CO and N2, 2 for all)
4 ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma
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 1.3674 4.0000 12.0000 2.0453 0.1444 0.9500 1.1706 4.0000
9.0000 1.5000 4.0000 27.5134 79.5548 5.0191 7.0500 0.0000
1.1168 0.0000 NaN 14.2732 24.4406 6.7313 0.8563 0.0000
-4.1021 5.0000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000
H 0.9479 1.0000 1.0080 1.1364 0.0232 0.9900 -0.1000 1.0000
9.0643 4.7746 1.0000 0.0000 121.1250 4.7757 9.7732 1.0000
-0.1000 0.0000 NaN 2.5194 2.3785 0.2223 1.0698 0.0000
-15.7683 2.1488 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
O 1.1939 2.0000 15.9990 1.9289 0.1201 0.9900 1.0981 6.0000
10.4842 8.2916 4.0000 28.8967 116.0768 7.9703 7.0500 2.0000
1.0479 20.0000 NaN 10.0338 2.2024 0.9942 0.9745 0.0000
-3.6141 2.7025 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000
N 1.3638 3.0000 14.0000 1.7000 0.0967 0.8537 1.1943 5.0000
9.8544 10.4284 4.0000 41.8891 100.0000 7.7391 7.5000 2.0000
1.0200 0.0700 NaN 1.5271 2.9480 2.6234 0.9745 0.0000
-5.6116 2.0047 1.0183 4.0000 2.5196 0.0000 0.0000 0.0000
10 ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(b
p(be2);p(bo3);p(bo4);n.u.;p(bo1);p(bo2)
1 1 80.8865 107.9944 52.0636 0.5218 -0.3636 1.0000 34.9876 0.7769
6.1244 -0.1693 8.0804 1.0000 -0.0586 8.1850 1.0000 0.0000
1 2 179.5195 0.0000 0.0000 -0.5242 0.0000 1.0000 6.0000 0.7187
5.4740 1.0000 0.0000 1.0000 -0.1144 6.7029 0.0000 0.0000
2 2 113.9232 0.0000 0.0000 -0.5971 0.0000 1.0000 6.0000 0.9093
1.7152 1.0000 0.0000 1.0000 -0.0450 6.0710 0.0000 0.0000
1 3 136.4945 164.1201 5.5000 -0.9159 -0.1075 1.0000 10.6519 0.8644
0.6858 -0.4602 9.5754 1.0000 -0.1745 4.5987 0.0000 0.0000
3 3 148.0798 155.2406 20.1160 -1.0000 -0.1254 1.0000 33.0027 0.7790
0.7673 -0.1697 7.0028 1.0000 -0.1300 5.1959 1.0000 0.0000
2 3 169.1351 0.0000 0.0000 -0.8810 0.0000 1.0000 6.0000 0.5757
1.5482 1.0000 0.0000 1.0000 -0.1788 4.6622 0.0000 0.0000
1 4 146.4220 161.9411 83.1445 -0.0673 -0.7385 1.0000 20.5574 0.3439
1.1554 -0.7615 6.3243 1.0000 -0.1692 5.3062 1.0000 0.0000
2 4 131.9942 0.0000 0.0000 -0.2031 0.0000 1.0000 4.0000 0.4507
10.2925 -0.3653 0.0000 1.0000 -0.0527 8.0000 0.0000 0.0000
3 4 78.7524 155.4183 100.4654 1.0000 -1.0000 1.0000 40.0000 0.1723
0.1607 -0.5703 5.5634 1.0000 -0.1969 4.9725 1.0000 0.0000
4 4 81.3043 99.0989 144.9704 -0.6110 -0.7864 1.0000 5.0000 0.1000
1.0202 -0.1368 8.0395 1.0000 -0.1463 3.8325 1.0000 0.0000
6 ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);r
1 2 0.1253 1.5717 9.9736 1.2057 -1.0000 -1.0000
2 3 0.1125 1.6311 8.7528 1.0929 -1.0000 -1.0000
1 3 0.0953 1.7397 8.8986 1.4256 1.1067 1.1265
1 4 0.1425 1.8737 10.3522 1.4256 1.3259 1.2082
2 4 0.0660 1.5027 8.8662 1.0548 -1.0000 -1.0000
3 4 0.1263 1.5263 10.0075 1.3841 1.2535 1.0000
41 ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);
1 1 1 76.1370 34.6920 1.1328 0.0000 0.0050 0.3556 1.8065
1 1 2 68.0572 9.9461 4.7000 0.0000 0.4566 0.0000 1.8532
2 1 2 65.6815 35.0000 1.8622 0.0000 0.0490 0.0000 1.0937
1 2 2 0.0000 4.0000 7.2043 0.0000 0.0000 0.0000 1.0728
1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
2 2 2 0.0000 30.0000 5.6235 0.0000 0.0000 0.0000 1.0400
1 1 3 78.3624 13.0773 9.0480 0.0000 0.1270 52.1129 2.3964
3 1 3 76.7101 24.3833 5.8613 -21.8559 2.6395 -32.6534 3.6179
2 1 3 79.1288 30.0000 1.4632 0.0000 0.2065 0.0000 2.0000
1 3 1 80.7352 16.4130 4.9987 0.0000 0.0843 0.0000 1.0137
1 3 3 85.4436 14.4937 3.9928 0.0000 1.4350 44.5320 1.1348
3 3 3 89.9282 32.1199 2.7181 0.0000 0.3323 57.6122 1.0000
1 3 2 82.9640 32.4874 0.8777 0.0000 0.9627 0.0000 1.0010
2 3 3 85.7838 17.3139 1.9157 0.0000 3.6306 0.0000 2.1858
2 3 2 84.2527 33.1226 0.6730 0.0000 0.7238 0.0000 2.4348
1 2 3 0.0000 14.4588 3.1507 0.0000 3.4571 0.0000 1.0149
3 2 3 0.0000 0.9696 3.6303 0.0000 0.0000 0.0000 1.6987
2 2 3 0.0000 0.5797 1.9739 0.0000 0.0000 0.0000 2.4494
1 1 4 89.5412 10.0000 3.1804 0.0000 0.1000 2.0000 2.0000
3 1 4 75.6717 34.2176 2.4651 0.0000 0.2576 0.0000 1.3080
4 1 4 56.7950 21.2889 1.1348 0.0000 0.1000 0.0000 2.0000
2 1 4 57.5770 16.8737 1.6684 0.0000 0.9500 0.0000 1.0100
1 2 4 0.0000 0.0100 5.6777 0.0000 0.0000 0.0000 1.2703
1 3 4 77.6218 14.9138 3.5216 0.0000 0.6416 0.0000 1.5611
3 3 4 87.1336 29.3985 2.1764 0.0000 0.6955 0.0000 1.8914
4 3 4 70.2689 19.9584 4.2797 0.0000 0.6998 0.0000 1.6913
2 3 4 73.7577 44.4943 0.5753 0.0000 3.0692 0.0000 1.5996
1 4 1 81.0255 35.0000 0.7103 0.0000 1.6888 0.0000 1.0100
1 4 3 90.0000 25.5053 4.4541 0.0000 2.1016 0.0000 1.2203
1 4 4 67.3194 22.7804 1.8415 0.0000 2.0063 0.0000 1.0100
3 4 3 74.8496 50.0000 1.6227 -6.6718 3.0000 50.0000 1.0100
3 4 4 74.6195 47.0693 0.9622 -3.4101 2.1852 0.0000 1.7988
4 4 4 66.6498 17.4122 7.0441 0.0000 1.1587 0.0000 1.2779
1 4 2 90.0000 20.9302 1.2522 0.0000 0.6402 0.0000 3.0000
2 4 3 83.0567 36.8198 1.0207 0.0000 0.8674 0.0000 3.0000
2 4 4 79.0108 22.2517 3.0204 0.0000 0.4118 0.0000 2.9985
2 4 2 49.0517 14.1263 7.4919 0.0000 0.1000 0.0000 1.0100
1 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
3 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
4 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
30 ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);n
1 1 1 1 2.0474 32.6719 0.5282 -9.0000 -2.6449 0.0000 0.0000
1 1 1 2 1.6328 78.4995 -0.1514 -6.9161 -2.9986 0.0000 0.0000
2 1 1 2 2.4142 78.7025 0.3506 -8.8640 -6.9283 0.0000 0.0000
1 1 1 3 -0.7104 22.6038 0.5309 -2.0000 -0.6614 0.0000 0.0000
2 1 1 3 1.9323 52.9368 0.6554 -8.8118 -3.9854 0.0000 0.0000
3 1 1 3 -1.2500 1.1248 -0.1230 -9.9453 -3.9000 0.0000 0.0000
......

作者
Author: 456321789 时间: 2023-8-29 20:26
请问，这个有什么办法可以解决吗？

作者
Author: 456321789 时间: 2023-8-29 20:27
还有一个问题，Lamms跑反应力场时，涉及化学键断裂和重组的反应，一定需要删除模型里的化学键吗？

作者
Author: sobereva 时间: 2023-8-30 00:22

456321789 发表于 2023-8-29 20:26
请问，这个有什么办法可以解决吗？

有别人回复之前若需要对帖子进行修改、补充，应直接编辑原帖，不要通过回帖进行补充，这点在置顶的新社员必读贴里明确说了。

作者
Author: wildon 时间: 2023-9-8 22:27
你好，可以看下我的关于ReaxFF建模的帖子，希望对你有所帮助

作者
Author: Graphite 时间: 2023-9-9 14:56
REAXFF中同种元素的原子类型是不额外分的，也就是说，碳就是碳，不分什么烷基碳/羰基碳...等等。
正对你的体系，在lammps中将9种原子类型设为 C O C C N N O H H即可。

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