Calculate MSDs during MD run

[Marcella Iannuzzi]

Hi Johannes

I tried your input and it runs fine, I did not get any segmentation fault.
As expected two output files are written, one per kind, with the MSD 
For kind 2:

      0       0.000        0.0000000000        0.0000000000        
0.0000000000        0.0000000000

       1       1.000        0.0000202689        0.0000306356        
0.0000178320        0.0000687364

       2       2.000        0.0000739085        0.0001240880        
0.0000741001        0.0002720966

       3       3.000        0.0001532087        0.0002815130        
0.0001712799        0.0006060016

       4       4.000        0.0002589779        0.0005096011        
0.0003126593        0.0010812382

Kind regards
Marcella


On Monday, August 3, 2015 at 4:08:09 PM UTC+2, Johannes Wagner wrote:
>
>
>
> Here are my input files:
>
> runtime_cp2k is the main input
> ref0.xy contains the reference coordinates
> reftraj.xyz contains the trajectory from a previous run.
>
> all I get is a segmentation fault and I am not sure where to look for the 
> error..
>
>
> Am Montag, 3. August 2015 14:22:33 UTC+2 schrieb Johannes Wagner:
>>
>> Hi Marcella,
>>
>> I figured that, finding
>> REF0_FILENAME 
>> under &MSD
>>
>> however the error remains the same.
>> What format do both, the REF0 and the trajectory, need to have? both are 
>> XMOL in my case, one containing the entire trajectory, the other only the 
>> first step
>> like this 
>>
>> ref0.xyz
>>       Cryst x
>>  i =        0, time =        0.000, E =       -16.1066791009
>>   O         4.4494725764        0.8609855793        6.0981987308
>>   O         3.8029095709        2.7229831166        4.5699381898
>>   O         4.0118989226        2.7023681308        1.2194938263
>>   O         6.0462348498        3.2953089592        5.9203028333
>>   O         3.2241009956        5.5031225318        4.3400008035
>> ..
>> ..
>>
>>
>>
>>
>> Am Montag, 3. August 2015 11:23:12 UTC+2 schrieb Marcella Iannuzzi:
>>>
>>> Hi
>>>
>>> The MSD calculation with REFTRAJ needs a 
>>> Reference coordinates file
>>>
>>> Regards
>>>
>>> Marcella 
>>>
>>>
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