[CP2K-user] Calculate MSDs during MD run

[Renjith S Pillai]

Hi,

Could you please help me, whenever I use the same files as that you used 
for the MSD, I am getting the segmentation fault as copied below and my 
cp2k version is the latest one, cp2k 6.1, I don't know why the segmentation 
fault for the already tested input files.


[hn1-srmhpc06:161286:0:161286] Caught signal 11 (Segmentation fault: Sent 
by the kernel at address (nil))
==== backtrace ====
 0 0x000000000067c69c __reftraj_util_MOD_compute_msd_reftraj()  
/home/rpillai/Libraries/cp2k-install/src/motion/reftraj_util.F:364
 1 0x0000000000777d0d __integrator_MOD_reftraj()  
/home/rpillai/Libraries/cp2k-install/src/motion/integrator.F:1629
 2 0x00000000006811f8 __velocity_verlet_control_MOD_velocity_verlet()  
/home/rpillai/Libraries/cp2k-install/src/motion/velocity_verlet_control.F:90
 3 0x000000000063b245 __md_run_MOD_qs_mol_dyn_low()  
/home/rpillai/Libraries/cp2k-install/src/motion/md_run.F:473
 4 0x000000000063bcd5 __md_run_MOD_qs_mol_dyn()  
/home/rpillai/Libraries/cp2k-install/src/motion/md_run.F:152
 5 0x00000000004ea237 __cp2k_runs_MOD_cp2k_run()  
/home/rpillai/Libraries/cp2k-install/src/start/cp2k_runs.F:356
 6 0x00000000004ed4c2 __cp2k_runs_MOD_run_input()  
/home/rpillai/Libraries/cp2k-install/src/start/cp2k_runs.F:1103
 7 0x00000000004e70db MAIN__()  
/home/rpillai/Libraries/cp2k-install/src/start/cp2k.F:281
 8 0x000000000043a3bd main()  
/home/rpillai/Libraries/cp2k-install/obj/local/popt/cp2k.F90:45
 9 0x0000000000022445 __libc_start_main()  ???:0
10 0x00000000004e695c _start()  ???:0
===================
Segmentation fault (core dumped)




 CP2K| version string:                                          CP2K 
version 6.1
 CP2K| source code revision number:                                    
svn:18464
 CP2K| cp2kflags: libint fftw3 libxc parallel mpi3 scalapack xsmm 
libderiv_max_a
 CP2K|            m1=5 libint_max_am=6
 CP2K| is freely available from                            
https://www.cp2k.org/
 CP2K| Program compiled at                          Wed Jul  3 15:39:08 IST 
2019
 CP2K| Program compiled on                                          
hn1-srmhpc06
 CP2K| Program compiled for                                                
local
 CP2K| Data directory path            
 /home/rpillai/Libraries/cp2k-install/data
 CP2K| Input file name                                          
runtime_cp2k.inp


Thanks in advance
renjith


On Monday, August 10, 2015 at 3:25:04 PM UTC+5:30, Marcella Iannuzzi wrote:
>
> 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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