output trajectory not periodic by setting "PERIODIC XYZ-POISSON"

[lizzy bai]

Dear Users,

I am new to CP2K.

Now I am simulating the water-air system using AIMD.

In my input file, I set the keywords below. However, the output trajectory not periodic in any directions.

  &POISSON

       PERIODIC XYZ 

    &END

Does anyone know how to solve this problem? Thank you very much for any suggestion in advance.

Best Wishes

Liyi Bai

[Vladimir Rybkin]

Dear Liyi Bai,

the .xyz files are unwrapped. And they should not look periodic as they represent only one (unit) cell. So, there's no problem.

Yours,

Vladimir

четверг, 12 декабря 2019 г., 11:51:08 UTC+1 пользователь lizzy bai написал:

[lizzy bai]

Dear  Vladimir.

Thank you very much for your reply.

However, when I follow the exercise"AbMD of bulk water", the output xyz format trajectory can show the periodic along xyz. So I don't know what is happening.

Thank you 

Best regards

Liyi

Vladimir Rybkin <rybk...@gmail.com> 于2019年12月12日周四 下午10:25写道：

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[lizzy bai]

Dear Prof. Travis

Thank you very much for your information. 

I set the output format as DCD , the file can not visualize via VMD. 

I am not sure if the VMD support the CP2K DCD trajectory file or not.

Best regards

Liyi Bai

Travis <polla...@gmail.com> 于2019年12月13日周五 上午11:24写道：

Hi,

XMOL (XYZ) format conatins no info about the lattice. The file in the example lists parameters in the title/comment line. This isn't read in any meaningful way in most visualization programs. If you want lattice info, save your trajectories in the future in DCD format. If you ran an NVT simulation your lattice is the same one from your input file, so you can add that via the console in VMD for all frames. If you ran NPT, you should look for a similar question to yours elsewhere in the forums. It has Python code that will read the CELL and XYZ file from CP2K and output a Gromacs style file that contains lattice data.

-T

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[lizzy bai]

Dear Prof. Travis

Thank you very much for you information.

I have formated the trajectory as DCD. Then the outfile only has DCD file, no xyz file. The following keywords I used as below:

 &TRAJECTORY

       FORMAT DCD
     &EACH
       MD 1
     &END EACH
   &END TRAJECTORY

Best regards

Liyi

Travis <polla...@gmail.com> 于2019年12月13日周五 下午10:45写道：

Hi,

You load an XYZ first. Then load DCD as additional data. DCD doesn't contain atom names.

-T

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[lizzy bai]

Dear Prof.Travis

Thank you very much for you reply.

Sorry, I have understood your points? "Convert the coordinates in your input file to XYZ." Here what kind of input are you mentioning?

I tried load the DCD and then load the xyz file. Then the the VMD displayed like below.

Previously, I tried  load the lammps output  DCD file along with the psf file, it woks well.

But for the cp2k output DCD, it doesn't work.

And, may I know it is possible to output both DCD and xyz files in CP2K?

Thank you very for your help

best regards

Liyi

Travis <polla...@gmail.com> 于2019年12月14日周六 下午5:19写道：

Hi,

Convert the coordinates in your input file to XYZ. You need only a single snapshot. Then load the XYZ into VMD and select to load additional data into the molecule to append the DCD. The XYZ file is used just to add the atom names. You can also use one of the snapshots from your old XYZ trajectory to do this.

-T

On Saturday, December 14, 2019 at 3:04:56 AM UTC-5, lizzy bai wrote:

Dear Prof. Travis

Thank you very much for you information.

I have formated the trajectory as DCD. Then the outfile only has DCD file, no xyz file. The following keywords I used as below:

 &TRAJECTORY

       FORMAT DCD
     &EACH
       MD 1
     &END EACH
   &END TRAJECTORY

Best regards

Liyi

Travis <polla...@gmail.com> 于2019年12月13日周五 下午10:45写道：

Hi,

You load an XYZ first. Then load DCD as additional data. DCD doesn't contain atom names.

-T

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[lizzy bai]

Dear Prof.Travis

Thank you very much for your help and patience.It works now.

Have a nice day

Best regards

Liyi

Travis <polla...@gmail.com> 于2019年12月15日周日 下午7:05写道：

Hi,

You've just loaded your coordinates incorrectly. Load XYZ first. Right click the line water-1.xyz, select Load Data Into Molecule. Ensure water-1.xyz is the molecule that is selected in the drop down menu. The default option in the Load Menu is to create a new molecule. Now just load the DCD. You will have a total number of frames equal to the number of frames in the DCD + 1 for the XYZ. You can print also to PDB which includes lattice, coordinate, and atom name data but sacrifices some precision as it writes fewer decimal places.

-T

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