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胡博洋的洋金蟲 (小有名氣)
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[求助]
經(jīng)過MS模型導(dǎo)入到LAMMPS，在運算時出現(xiàn)的錯誤求助 已有2人參與
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我的模型是從MS軟件中導(dǎo)出來的，力場設(shè)置的是cvff，用LAMMPS中的msi2lmp工具導(dǎo)出data文件。data文件我也認真看了，沒有錯誤。但是我在提交LAMMPS運算時出現(xiàn)了如下情況： ------------------------------------------------------------------------------------------------------ LAMMPS (22 Mar 2013) Scanning data file ... 25 = max angles/atom 88 = max dihedrals/atom Reading data file ... orthogonal box = (0 0 0) to (10.4507 6.0874 4.752) 4 by 2 by 2 MPI processor grid 28 atoms 116 angles 272 dihedrals Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors 4 atoms in group 1 16 atoms in group 2 4 atoms in group 3 4 atoms in group 4 Replicating atoms ... orthogonal box = (0 0 0) to (31.3521 18.2622 14.256) 4 by 2 by 2 MPI processor grid 756 atoms 3132 angles 7344 dihedrals Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors WARNING: Resetting reneighboring criteria during minimization (min.cpp:173) Ewald initialization ... G vector (1/distance) = 0.284516 estimated absolute RMS force accuracy = 0.000147646 estimated relative force accuracy = 1.02535e-05 KSpace vectors: actual max1d max3d = 731 10 4630 Setting up minimization ... Memory usage per processor = 36.3555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -29439.954 139654.04 110214.08 -1054599.1 43 0 -3.625706e+16 88135.753 -3.625706e+16 -2.3722708e+18 Loop time of 1.14906 on 16 procs for 43 steps with 756 atoms Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = 110214.082772 -3.62570600766e+16 -3.62570600766e+16 Force two-norm initial, final = 5892.7 1.29073e+31 Force max component initial, final = 355.236 8.16331e+30 Final line search alpha, max atom move = 9.9195e-74 8.0976e-43 Iterations, force evaluations = 43 424 Pair time (%) = 0.652155 (56.7553) Bond time (%) = 0.0531141 (4.62238) Kspce time (%) = 0.35794 (31.1505) Neigh time (%) = 0.00358602 (0.312082) Comm time (%) = 0.0253774 (2.20853) Outpt time (%) = 0 (0) Other time (%) = 0.0568924 (4.9512) Nlocal: 47.25 ave 56 max 41 min Histogram: 2 2 1 1 2 4 2 1 0 1 Nghost: 4239.88 ave 4298 max 4175 min Histogram: 3 2 3 0 0 0 0 0 3 5 Neighs: 49139.7 ave 58021 max 42819 min Histogram: 2 3 0 2 1 6 0 1 0 1 Total # of neighbors = 786235 Ave neighs/atom = 1039.99 Ave special neighs/atom = 0 Neighbor list builds = 2 Dangerous builds = 0 Ewald initialization ... G vector (1/distance) = 0.284516 estimated absolute RMS force accuracy = 0.000147646 estimated relative force accuracy = 1.02535e-05 KSpace vectors: actual max1d max3d = 731 10 4630 Setting up run ... Memory usage per processor = 36.5856 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -3.625706e+16 88135.753 -3.625706e+16 -2.3722708e+18 8162.3914 APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) ------------------------------------------------------------------------------------------------------ 當我把minimize 命令去掉后，出現(xiàn)如下問題： ------------------------------------------------------------------------------------------------------ LAMMPS (22 Mar 2013) Scanning data file ... 25 = max angles/atom 88 = max dihedrals/atom Reading data file ... orthogonal box = (0 0 0) to (10.4507 6.0874 4.752) 4 by 2 by 2 MPI processor grid 28 atoms 116 angles 272 dihedrals Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors 4 atoms in group 1 16 atoms in group 2 4 atoms in group 3 4 atoms in group 4 Replicating atoms ... orthogonal box = (0 0 0) to (31.3521 18.2622 14.256) 4 by 2 by 2 MPI processor grid 756 atoms 3132 angles 7344 dihedrals Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors Ewald initialization ... G vector (1/distance) = 0.284516 estimated absolute RMS force accuracy = 0.000147646 estimated relative force accuracy = 1.02535e-05 KSpace vectors: actual max1d max3d = 731 10 4630 Setting up run ... Memory usage per processor = 36.7132 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 -29439.954 139654.04 110214.08 -1054599.1 8162.3914 100 17.156213 -27586.553 82839.726 55254.847 189936.49 7175.6492 ERROR on proc 4: Angle atoms 35 54 45 missing on proc 4 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ERROR on proc 1: Angle atoms 511 530 521 missing on proc 1 at step 136 (neigh_bond.cpp:168) ERROR on proc 5: Angle atoms 539 558 549 missing on proc 5 at step 136 (neigh_bond.cpp:168) ERROR on proc 6: Angle atoms 203 222 213 missing on proc 6 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 ERROR on proc 0: Angle atoms 7 26 17 missing on proc 0 at step 136 (neigh_bond.cpp:168) ERROR on proc 9: Angle atoms 632 643 627 missing on proc 9 at step 136 (neigh_bond.cpp:168) ERROR on proc 11: Angle atoms 716 727 711 missing on proc 11 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11 ERROR on proc 3: Angle atoms 679 698 689 missing on proc 3 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3 ERROR on proc 8: Angle atoms 380 391 375 missing on proc 8 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8 ERROR on proc 12: Angle atoms 72 83 67 missing on proc 12 at step 136 (neigh_bond.cpp:168) ERROR on proc 13: Angle atoms 576 587 571 missing on proc 13 at step 136 (neigh_bond.cpp:168) ERROR on proc 2: Angle atoms 175 194 185 missing on proc 2 at step 136 (neigh_bond.cpp:168) ERROR on proc 10: Angle atoms 464 475 459 missing on proc 10 at step 136 (neigh_bond.cpp:168) ERROR on proc 14: Angle atoms 240 251 235 missing on proc 14 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13 ERROR on proc 7: Angle atoms 707 726 717 missing on proc 7 at step 136 (neigh_bond.cpp:168) ERROR on proc 15: Angle atoms 744 755 739 missing on proc 15 at step 136 (neigh_bond.cpp:168) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 10 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 15 ------------------------------------------------------------------------------------------------------ 當我刪掉一些angles（即不考慮某些作用角）時卻可以正常運行，計算出結(jié)果，如果我想考慮全部的鍵角就會錯誤，所以在此懇求各位前輩，幫我看看可以怎么解決感激不盡~！ |
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【答案】應(yīng)助回帖
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月只藍: 金幣+1, 感謝指導(dǎo)！ 2014-05-16 18:31:19
月只藍: 金幣+1, 感謝指導(dǎo)！ 2014-05-16 18:31:19
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1、VMD可以從六維等網(wǎng)站下載，然后熟悉一下基本的VMD基本的操作就可以了，不用學(xué)的太復(fù)雜。 2、MS導(dǎo)出pdb格式，然后導(dǎo)入VMD，然后用topo writelammpsdata命令轉(zhuǎn)化成lammps所需的data文件 3、lammps中使用dump ~ ~ atom ~ dump.lammpstrj命令產(chǎn)生軌跡文件，次文件可以直接導(dǎo)入VMD，并且有動態(tài)效果 |
7樓2014-05-04 11:02:15
飛利白
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139564@chen
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2樓2013-12-29 16:55:42
胡博洋的洋
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ashioulou
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胡博洋的洋: 金幣+10, ★★★很有幫助, 謝謝~，最近較忙，一直沒去試 2014-01-02 10:03:51
月只藍: 金幣+1, 感謝指導(dǎo)。 2014-01-02 10:42:06
胡博洋的洋: 金幣+10, ★★★很有幫助, 謝謝~，最近較忙，一直沒去試 2014-01-02 10:03:51
月只藍: 金幣+1, 感謝指導(dǎo)。 2014-01-02 10:42:06
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??????N????}???????????????^???????????y?\????? ?????????N??in?????????^???????????N???} ????????Q???k?????? 1. ?S??minimize???????y??????С?????\????C 2. ??_???timestep?{С??c????Εr?g |
4樓2013-12-30 10:00:42
5樓2014-01-02 09:31:30
wdwangcn
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6樓2014-05-02 18:27:33
飛利白
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8樓2014-09-22 10:43:34
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