[CP2K-user] [CP2K:17697] Re: CP2K Cell Boundary Coordinates

Nam Tran trannamphys at gmail.com
Fri Sep 16 04:59:23 UTC 2022


Why the cell vectors in your POSCAR are different with your CP2K input file?
Also it is not CUBIC cell.


On Thursday, 15 September 2022 at 2:47:08 am UTC+8 qkn... at gmail.com wrote:

> Hi, 
> I tried a NPT MD , but it fails with an errors saying, An invalid set of 
> cell vectors was specified. The determinant  det(h) is too small. I am 
> attaching the input files, logs and other files. Will someone have a look 
> to point out the error in the input file? 
> Thanks
> Dev
> On Tuesday, September 13, 2022 at 10:04:54 AM UTC-4 Dev Kumar wrote:
>> Thanks for responding. Thats standard steps we use in LAMMPS MD 
>> simulations also. I will try it out. 
>> On Tuesday, September 13, 2022 at 9:49:29 AM UTC-4 mattwa... at gmail.com 
>> wrote:
>>> Well before you run NPT you need to check that you can converge the 
>>> electron structure and that there are no large forces present in the system.
>>> As for any MD I'd suggest a typical workflow would be at least a rough 
>>> geometry optimization. Then NVT then switch to NPT.
>>> NPT might need rather tight settings to have a well converged stress 
>>> tensor.
>>> Matt
>>> On Tuesday, 13 September 2022 at 14:23:57 UTC+1 qkn... at gmail.com wrote:
>>>> HI Matt, 
>>>> Thanks for your reply. I attached the POSCAR. I am new to cp2k and I 
>>>> assumed that cp2k is taking the angles of the box 90 degrees and cubic. 
>>>> This is just my lack of knowledge. This is cubic fcc cell, I can 
>>>> give ALPHA_BETA_GAMMA 90.00000000 90.00000000  90.00000000   SYMMETRY CUBIC 
>>>> inside cell. I will try that out. Although I will still need to make sure 
>>>> cp2k taking all the atoms inside the boundary. I may need to leave some 
>>>> vacuum sometimes, so I should be able to manipulate the box size. Please 
>>>> let me know you comments. 
>>>> When I look at the output position file it does look like its printing 
>>>> out from the initial position I started with, but becomes mushy after few 
>>>> steps of geometry optimization. 
>>>> On Tuesday, September 13, 2022 at 8:40:40 AM UTC-4 mattwa... at gmail.com 
>>>> wrote:
>>>>> I'm afraid I can't remember all Lammps' conventions - it would also 
>>>>> depend on system of units used in the data file etc
>>>>> Can you get ovito to also output a PDB or POSCAR or something you can 
>>>>> check against.
>>>>> Also, If you are running DFT you will want something closer to a cubic 
>>>>> cell if possible - and it might need to be quite large if your allow is 
>>>>> metallic...
>>>>> Matt
>>>>> On Monday, 12 September 2022 at 15:28:19 UTC+1 qkn... at gmail.com wrote:
>>>>>> Hi Experts, 
>>>>>> I am new cp2k user. I am trying to simulate a MD simulation on a 
>>>>>> metallic alloy and it keeps failing to start a NPT MD. I have a question 
>>>>>> about the structure boundaries in CP2K. I created the initial box in lammps 
>>>>>> and visualizing in ovito. Below are the box sizes. Am I converting it 
>>>>>> correctly for the cp2k simulation. 
>>>>>> *# LAMMPS data file written by OVITO*
>>>>>> 208 atoms
>>>>>> 3 atom types
>>>>>> -0.104644 20.6326618 xlo xhi
>>>>>> -19.8380928 19.8555032 ylo yhi
>>>>>> -0.0701645 2.082567 zlo zhi
>>>>>> *! CP2K Format*
>>>>>>  &CELL
>>>>>>       A   21.4280004501         0.0000000000         0.0000000000
>>>>>>       B   0.0000000000         42.9860000610         0.0000000000
>>>>>>       C   0.0000000000         0.0000000000        4.2329998016
>>>>>>       PERIODIC  XYZ 
>>>>>>     &END CELL
>>>>>>     &TOPOLOGY
>>>>>>       COORD_FILE_NAME AlCuMg.xyz
>>>>>>     &END
>>>>>> Thanks
>>>>>> Dev Kumar
>>>>>> Brown University
>>>>>> Providence, RI 

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