[CP2K:7613] Re: how to keep the atom's trajectory within the box

[王胜杰]

Dear Huan,

Thanks for your instruction. I have tried your method about VMD, it works. 
Although  VMD can only handle a little piece of trajectory, it can prove my 
thought and my program is right at least.

In fact, I already have written a program to deal with the real trajectory, 
making it within the box. I just find my method is  troublesome. I think 
that dealing the problem during MD is much better than after treatment.


Best wishes,
Shengjie

在 2016年3月25日星期五 UTC+8上午4:26:48，Huan Wang写道：
>
> Hi Shengjie,
>
> VMD is able to load short segment of the trajectory. You do not need to 
> load the whole trajectory if the file is larger than the memory of your 
> computer.
>
> Since you have known the possible step point that the atom might move out 
> of the box based on your own program (script), it is a good idea to check 
> the trajectory around this point by using VMD. 
> For example, if the step point is the 23456th frame, you can only load 100 
> points before and after this frame. e.g. from 23356 to 23556. Please see 
> the picture below on which the red box and ellipse indicating the key 
> points you need to pay attention. 
>
> [image: Inline image 1]
>  
> After loading the segment of your trajectory, you need to set the pbc box 
> length and wrap the atoms as I suggested in the last response.
> Visualization the results will help you check both the trajectory and your 
> program (script).
>
> Good luck.
>
> Huan
> .
>
>
>
> On Thu, Mar 24, 2016 at 5:37 PM, 王胜杰 <theanci... at gmail.com 
> <javascript:>> wrote:
>
>> Dear Huan,
>>
>> I didn't display the trajectory, because the trajectory file is really 
>> big, thus it can't be dragged to VMD.  I wrote a little program 
>> to identify it. First I found the min and max coordinates in the initial 
>> configuration, in ensemble NVT, when the atom coordinates less than min or 
>> larger than max, identify it crossing the boundary. And print out which 
>> atom and during which step.
>> Sure I can split the trajectory into several parts, but splitting costs 
>> too much time, and VMD always crash.
>>
>> Best wishing,
>> Shengjie Wang 
>> .
>> 在 2016年3月24日星期四 UTC+8下午6:07:21，Huan Wang写道：
>>>
>>> Hi Shengjie,
>>>
>>> An additional question is how do you display the trajectory? 
>>> If you use VMD, then you need to type some codes in *Extensions --> Tk 
>>> console* to let the VMD know the size of your simulation box.
>>>
>>> The codes are:
>>>
>>> pbc set {xxx xxx xxx} -all 
>>> # Here the "xxx" is the length of your (cubic) box. And "-all" means 
>>> this operation controls all frames in the current trajectroy.
>>> pbc box
>>> pbc wrap -all 
>>> # The wrap commend will show the atoms on the other side of the box when 
>>> atoms move out of the box.
>>>
>>> Good luck,
>>> Huan
>>> .
>>>
>>> On Thu, Mar 24, 2016 at 3:39 AM, 王胜杰 <theanci... at gmail.com> wrote:
>>>
>>>> Hi Huan,
>>>>
>>>> Thanks for your attention.
>>>> Yes, I did. I noticed and added the keyword the PERIODIC, and I tried 
>>>> the ensemble NPT_I and NVT, but cp2k still printed a real trajectory.
>>>>
>>>> Regards,
>>>> Shengjie Wang
>>>>
>>>> 在 2016年3月23日星期三 UTC+8上午4:45:33，hua... at mail.huji.ac.il写道：
>>>>
>>>>> Hi Shengjie,
>>>>>
>>>>> Did you specify the keyword PERIODIC in the &SUBSYS &CELL section?
>>>>> Please see the CP2K manual
>>>>>  
>>>>> https://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#PERIODIC
>>>>>
>>>>> Regards,
>>>>> Huan
>>>>> .
>>>>>
>>>>> On Friday, March 18, 2016 at 6:41:41 PM UTC+2, 王胜杰 wrote:
>>>>>>
>>>>>> Dear all
>>>>>>
>>>>>> When I was dealing with the trajectory of MD, I found the atoms 
>>>>>> always move beyond the boundary, making some atoms' coordinate larger than 
>>>>>> the box length,which reflect the true trajectories. 
>>>>>> But I don't want a true trajectory, I want a periodic boundary.When 
>>>>>> the atoms cross the boundary, the coordinate will minus the box length 
>>>>>> automatically, which each direction of  atoms' coordinate is less than the 
>>>>>> box length. By adding what command line can I fix that?
>>>>>>
>>>>>> Thanks in advance.
>>>>>> Shengjie Wang 
>>>>>>
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