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本帖最后由 ddddnight 于 2024-9-6 14:52 编辑
老师们好,我在用lammps使用reaxff力场模拟热解过程,模拟开始分子就全散开了,第0帧也就是原始的结构还保持线性结构,第一帧(1000fs)就全部散开了,这是怎么回事呢?
我是这么做的:
1. 首先用gaussview建立有机高分子模型(PP,聚丙烯,64个重复单元),然后用xtb在GFN2-xtb2进行了结构优化
2.将优化后的结构使用packmol建立了100*100*100的立方盒子,填充了40个分子(填充了20/30/15个分子也还会这样散开),保存pdb格式
3.将产生的盒子模型导入到vmd中,通过
mol bondsrecalc top
topo retypebonds
topo guessangles
mol reanalyze top
topo writelammpsdata <filename> charge
命令产生data命令,期间也只尝试topo writelammpsdata <filename> charge命令生成过data文件,分子还是会散开
4.通过产生的data文件,结合lammps中reaxff文件中的关于C、H、O、N、S元素的力场文件,Guo W, Fan K, Guo G, et al. Atomic-scale insight into thermal decomposition behavior of polypropylene: A ReaxFF method[J]. Polymer Degradation and Stability, 2022, 202: 110038.
HE X, CHEN D. ReaxFF MD study on the early stage co-pyrolysis of mixed PE/PP/PS plastic waste[J]. Journal of Fuel Chemistry and Technology, 2022, 50(3): 346-356.
根据这两篇文献中的方法,但是无论是npt还是nvt都会散开,data文件、前面几帧的xyz文件、dump文件已经上传网盘。
通过百度网盘分享的文件:dump-traj-data.zip
链接:https://pan.baidu.com/s/1S9A3CR-GQ4JDfHv3_LTD3w?pwd=alwr
提取码:alwr
1 0 -2653438.1 0 -2653438.1 45555.708 1000000
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 2: (0.0009448834682562179, 0) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 3: (0.0004989838657328307, 0.00024252561420354246) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 4: (0.001197736134366707, 6.66790795126025e-05) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 5: (0.0016731685137087108, 0.0002775626746108487) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 6: (0.0007615643931525492, 0.00039965754849295563) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 7: (0.002230955291605522, 0.00043335857143533943) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
WARNING: Fix qeq/reaxff/kk cg_solve convergence failed after 200 iterations at step 8: (8.147526483379655e-05, 0) (src/KOKKOS/fix_qeq_reaxff_kokkos.cpp:818)
1000 1799.7224 -2794869.3 0 -2649493.2 1762.6241 1006098.8
2000 1556.382 -2790410.8 0 -2664690.9 1787.773 1014611.9
3000 1418.5371 -2794696.9 0 -2680111.8 1117.8121 1020575.4
4000 1289.7053 -2798883.7 0 -2694705.2 741.89911 1025312.9
5000 1199.4079 -2805199.2 0 -2708314.6 655.02696 1029406.6
6000 1118.6466 -2810663.9 0 -2720303 987.42722 1032918.8
7000 1026.5642 -2814577.9 0 -2731655.1 511.06019 1035792.9
8000 960.16552 -2819624 0 -2742064.8 844.24895 1038230.2
9000 898.06142 -2824196.5 0 -2751653.8 -12.431105 1040270.9
10000 838.72496 -2828253.1 0 -2760503.5 300.23484 1042083.9
11000 781.40282 -2831652.7 0 -2768533.4 -17.954562 1043688.9
12000 740.21386 -2835721.8 0 -2775929.6 918.37852 1045102.3
13000 695.13768 -2838855.6 0 -2782704.4 176.51 1046405.1
14000 659.90563 -2842267.3 0 -2788962.1 40.647696 1047615.3
15000 625.56836 -2845242.6 0 -2794711.1 -145.57239 1048679.1
16000 592.63368 -2847910.7 0 -2800039.6 621.29481 1049616.9
17000 566.62083 -2850762 0 -2804992.1 -518.73604 1050502.1
18000 537.11887 -2852864.1 0 -2809477.2 -194.56289 1051253.1
19000 512.9524 -2855087.8 0 -2813653.1 -392.45229 1051952.9
20000 485.45974 -2856715.1 0 -2817501.1 -284.92156 1052551.2
21000 466.67518 -2858729.5 0 -2821032.9 341.47235 1053070.9
22000 444.46713 -2860212.8 0 -2824310.1 75.07647 1053537
23000 426.12225 -2861801.7 0 -2827380.9 590.60469 1053941.2
24000 411.59776 -2863439.9 0 -2830192.3 -99.370979 1054307
25000 395.3957 -2864756 0 -2832817.1 624.41199 1054614.5
26000 383.17163 -2866177 0 -2835225.6 156.63848 1054905
27000 365.95519 -2866979.7 0 -2837418.9 -402.77025 1055131.5
28000 356.74283 -2868294.9 0 -2839478.3 -13.680582 1055302
29000 343.79546 -2869190.9 0 -2841420.1 581.54303 1055425.8
30000 333.45303 -2870118 0 -2843182.6 79.722752 1055552.1
31000 325.28392 -2871112.1 0 -2844836.6 362.68944 1055654.2
32000 315.09877 -2871785.7 0 -2846333 577.2486 1055758.4
33000 304.91378 -2872300.9 0 -2847670.9 -104.80897 1055815.3
34000 301.68821 -2873310.2 0 -2848940.8 35.654605 1055841
35000 291.00447 -2873602.8 0 -2850096.3 -82.906384 1055806.5
36000 288.31074 -2874445.5 0 -2851156.6 -559.7815 1055745.6
37000 280.6496 -2874735.2 0 -2852065.2 656.01444 1055668.5
38000 280.57994 -2875557.6 0 -2852893.2 255.67349 1055573.1
39000 275.09416 -2875858.4 0 -2853637.1 375.72877 1055491.2
40000 274.59842 -2876427.2 0 -2854246 -41.939107 1055424.3
这是log文件部分,没有收敛警告也还是会散开,是不是因为这个压力的原因
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1帧.png
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0帧.png
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ffield.reax.PP
14.79 KB, 下载次数 Times of downloads: 2
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in.PPbox1
647 Bytes, 下载次数 Times of downloads: 6
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lmp_control
405 Bytes, 下载次数 Times of downloads: 2
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log.lammps
28.99 KB, 下载次数 Times of downloads: 1
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packmol.inp
119 Bytes, 下载次数 Times of downloads: 1
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param.qeq
49 Bytes, 下载次数 Times of downloads: 2
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