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胡博洋的洋

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[求助] 经过MS模型导入到LAMMPS，在运算时出现的错误求助已有2人参与

我的模型是从MS软件中导出来的，力场设置的是cvff，用LAMMPS中的msi2lmp工具导出data文件。data文件我也认真看了，没有错误。但是我在提交LAMMPS运算时出现了如下情况：
------------------------------------------------------------------------------------------------------
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)
------------------------------------------------------------------------------------------------------
当我把minimize 命令去掉后，出现如下问题：
------------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------------
当我删掉一些angles（即不考虑某些作用角）时却可以正常运行，计算出结果，如果我想考虑全部的键角就会错误，所以在此恳求各位前辈，帮我看看可以怎么解决感激不尽~！

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不得求之

1楼 2013-07-16 10:17:57

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笑笑愁

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未知

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【答案】应助回帖

★
月只蓝: 金币+1, 感谢指导！ 2014-05-16 18:31:19

引用回帖:

6楼: Originally posted by wdwangcn at 2014-05-02 18:27:33
请教vmd的方法，能给个链接么...

1、VMD可以从六维等网站下载，然后熟悉一下基本的VMD基本的操作就可以了，不用学的太复杂。
2、MS导出pdb格式，然后导入VMD，然后用topo writelammpsdata命令转化成lammps所需的data文件
3、lammps中使用dump ~ ~ atom ~ dump.lammpstrj命令产生轨迹文件，次文件可以直接导入VMD，并且有动态效果

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有志者，事竟成。

7楼2014-05-04 11:02:15

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飞利白

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引用回帖:

9楼: Originally posted by 笑笑愁 at 2014-09-22 11:05:25
vmd命令： topo writelammpsdata 文件名...

我试了一下，但是一会就没有反应了，如果正确的话是不是会提示保存在哪之类的呢。谢谢

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10楼2014-09-22 17:14:47

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普通回帖

139564@chen

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lz 你好，你的问题解决了嘛？我也遇到这个问题

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杂草就要用杂草的方式去生活

2楼2013-12-29 16:55:42

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木有解决····

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不得求之

3楼2013-12-29 20:16:47

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ashioulou

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★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
胡博洋的洋: 金币+10, ★★★很有帮助, 谢谢~，最近较忙，一直没去试 2014-01-02 10:03:51
月只蓝: 金币+1, 感谢指导。 2014-01-02 10:42:06

??????N????}???????????????^???????????y?\?????
?????????N??in?????????^???????????N???}
????????Q???k??????
1. ?S??minimize???????y??????С?????\????C
2. ??_???timestep?{С??c????Εr?g

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4楼2013-12-30 10:00:42

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