[CP2K-user] Molecules moving out of simulation cell in AIMD simulation

Travis polla... at gmail.com
Tue Oct 8 15:21:59 UTC 2019


Compile the code with your preferred Fortran compiler,
gfortran dumpdcd.f90

Run code on a host of DCD files you want to merge, these would be coming 
from a long simulation that you broke up into smaller segments,
./a.out -xyz reference.xyz -pbc -of dcd -o full_foo_trajectory.dcd foo1.dcd 
foo2.dcd foo3.dcd ... fooN.dcd

You need a reference XYZ format file for determining atom name as DCD only 
contains lattice parameters and coordinates. The -pbc flag says to produce 
a wrapped trajectory, while leaving it off produces the unwrapped 

To wrap an XYZ trajectory requires TRAVIS 
(https://www.travis-analyzer.de/). In one of the advanced options, you can 
read the second line for each frame of the XYZ file as the lattice 
parameters in Angstroms and degrees. I give a more detailed explanation of 
it here, https://groups.google.com/forum/#!topic/cp2k/GNLdTcUZFUo (for 
NPT). Alternatively, if you are comfortable with Python, you can use the 
Atomic Simulation Environment.


On Tuesday, October 8, 2019 at 4:23:27 AM UTC-3, farzaneh sarrami wrote:
> Thanks Travis,
> Would you please explain in more details how can I use dumpdcd.f90 script 
> in cp2k ? as I have same problem.
> Best,
> Farzaneh
> On Monday, October 7, 2019 at 5:01:01 PM UTC+2, Travis wrote:
>> Hi,
>> CP2K dumps unwrapped coordinates, so they are not imaged back into the 
>> box if they drift beyond. A simple way to get a wrapped trajectory is to 
>> dump DCD files during MD, then use the dumpdcd.f90 script in tools/ to dump 
>> a wrapped DCD (-pbc option). I don't recommend writing XYZ format 
>> trajectories for MD. Write DCD and convert. Way easier to strip info than 
>> to add it back in.
>> -T
>> On Monday, October 7, 2019 at 8:09:09 AM UTC-3, Harender Singh wrote:
>>> Dear all, 
>>> I am running AIMD simulation of some electrolyte at Li electrode. While 
>>> the electrolyte molecules are staying within the simulation cell, the 
>>> electrode atoms are moving out of the cell. 
>>> Is there any possible explanation for that?
>>> Is there something wrong with my simulation setup? If yes, then how can 
>>> I correct it?
>>> Thanks for the help in advance. 
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