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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » LAMMPS/DL_POLY » 如何把lammps的轨迹文件转化为视频呢？
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楼1970-01-01 08:00:00
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【答案】应助回帖

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月只蓝: 金币+2, 鼓励交流 2014-01-12 09:24:59
笑笑愁: 金币+3, ★★★很有帮助 2014-01-12 11:09:23
------- To view a lammps trajectory in VMD --------





1) Build a PSF file for use in viewing with VMD.



This step works with VMD 1.9 and topotools 1.2.  

(Older versions, like VMD 1.8.6, don't support this.)





a) Start VMD

b) Menu  Extensions->Tk Console

c) Enter:



(I assume that the the DATA file is called "system.data"



   topo readlammpsdata system.data full

   animate write psf system.psf



2)



Later, to Load a trajectory in VMD:



  Start VMD

  Select menu: File->New Molecule

-Browse to select the PSF file you created above, and load it.

  (Don't close the window yet.)

-Browse to select the trajectory file.

  If necessary, for "file type" select: "LAMMPS Trajectory"

  Load it.



   ----  A note on trajectory format: -----

If the trajectory is a DUMP file, then make sure the it contains the

information you need for pbctools (see below.  I've been using this

command in my LAMMPS scripts to create the trajectories:



  dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz



It's a good idea to use an atom_style which supports molecule-ID numbers

so that you can assign a molecule-ID number to each atom.  (I think this

is needed to wrap atom coordinates without breaking molecules in half.)



Of course, you don't have to save your trajectories in DUMP format,

(other formats like DCD work fine)  I just mention dump files

because these are the files I'm familiar with.



3) -----  Wrap the coordinates to the unit cell

          (without cutting the molecules in half)



a) Start VMD

b) Load the trajectory in VMD (see above)

c) Menu  Extensions->Tk Console

d) Try entering these commands:



    pbc wrap -compound res -all

    pbc box



    ----- Optional ----

    Sometimes the solvent or membrane obscures the view of the solute.

    It can help to shift the location of the periodic boundary box

    To shift the box in the y direction (for example) do this:



    pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}

    pbc box -shiftcenterrel {0.0 0.15 0.0}



    Distances are measured in units of box-length fractions, not Angstroms.



    Alternately if you have a solute whose atoms are all of type 1,

    then you can also try this to center the box around it:



    pbc wrap -sel type=1 -all -centersel type=2 -center com



4)

    You should check if your periodic boundary conditions are too small.

    To do that:

       select Graphics->Representations menu option

       click on the "Periodic" tab, and

       click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.



5) Optional: If you like, change the atom types in the PSF file so

   that VMD recognizes the atom types, use something like:



sed -e 's/   1    1      /   C    C      /g' < system.psf > temp1.psf

sed -e 's/   2    2      /   H    H      /g' < temp1.psf  > temp2.psf

sed -e 's/   3    3      /   P    P      /g' < temp2.psf  > system.psf



(If you do this, it might effect step 2 above.)


以上为lammps mailing list某位大神的回帖关于vmd如何读入lammps trajectory，读入之后就可以制作动画了。
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3楼2014-01-12 00:23:33
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茹此无声

木虫 (小有名气)

【答案】应助回帖

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感谢参与，应助指数 +1
月只蓝: 金币+2, 感谢指导 2014-01-11 07:32:05
笑笑愁: 金币+3, ★★★很有帮助 2014-01-11 14:40:13
在vmd中有个制作视频的，把图像文件导出来，再利用VM制作。

[ 发自小木虫客户端 ]
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人类一思考，上帝就发笑。
2楼2014-01-11 00:17:13
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