Re-optimising transition state using dimer method

[Matt W]

Hi,

try specifying the CP2K_INPUT <http://manual.cp2k.org/trunk/CP2K_INPUT.html>
 / MOTION <http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION.html> / GEO_OPT 
<http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/GEO_OPT.html> / 
TRANSITION_STATE 
<http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/GEO_OPT/TRANSITION_STATE.html>
 / DIMER 
<http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/GEO_OPT/TRANSITION_STATE/DIMER.html>
 / DIMER_VECTOR 
<http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/GEO_OPT/TRANSITION_STATE/DIMER/DIMER_VECTOR.html> section. 
You can take a vector from one of the minima to your TS guess,  (i.e. it 
will be a 3N vector) or from one of the NEB images to the TS. Maybe the 
imaginary frequency eigenvector would be best if you have it. That should 
make it much more likely the dimer goes uphill to the TS.

It is probably a good idea to experiment with a small system / cheaper 
Hamiltonian too.

Matt

On Tuesday, September 8, 2015 at 11:11:49 AM UTC+1, Tobias Kraemer wrote:
>
> Dear SL,
>
>
> thanks for clarification. The calculation did work now, however, the 
> outcome was somewhat unexpected. The structure converged to a minimum, 
> although I asked
> for a transition state optimisation. To be clear, the input geometry is 
> very close to a good transition state (it comes from a CI-NEB calculation). 
> The vibrational analysis revealed a prominent imaginary mode which 
> corresponds to the desired reaction channel. A second, much smaller (10s 
> cm-1) imagrinary mode was found, which involved a small rotation of a group 
> in the side chain. I want to get rid of this mode, and to this end, I 
> displaced the structure along the smaller imaginary mode (using the scaled 
> displacement vector from the vibrational analysis). I was hoping that with 
> such a good guess of the TS structure, it should be straightforward to 
> converge to the desired TS (with only one large imaginary mode). The fact 
> that the structure fell back into a minimum suggests to me, that I have 
> done something wrong. I have uploaded the input along with the starting 
> structure and the trajectory of the optimisation [note the structure is 
> quite large, the reaction happens at centre Rh(277)]. 
>
> I am particularly keen to learn which parameters I may have to change, or 
> if I am even providing the right input structure. From the test examples in 
> CP2K distribution it appears to me that providing one structure is 
> suffcient (these test cases ran without a problem, however, they are very 
> small systems).
>
> At this stage it would be crucial for me to work out the protocols for 
> running these type of calculations, since there are are number of TSs along 
> a complex pathway which I need to locate. I presume that the present case 
> won't be the only tricky TS which will need re-optimisation. As a note 
> aside, a constrained optimisation on the same system yielded the desired 
> TS, but this is only possible in cases, where the change in geometry does 
> not affect the core structure of the reaction coordinate to large extend. I 
> have dealt with situations in the meantime, where this method does not 
> work, and I would be relying on the dimer method.
>
> Thanks for your comments, much appreciated
>
>
> Cheers  
>
>
> Tobias
>   
>
>
>
>
> On Tuesday, September 1, 2015 at 5:11:13 PM UTC+1, Tobias Kraemer wrote:
>>
>> Hi all,
>>
>>
>> I am trying to re-optimise a transition state structure which has a 
>> spurious (small) imaginary mode on top of the large imaginary mode which 
>> corresponds to the transition state. I've also tested doing a constrained 
>> optimisation fixing selected atoms involved in the transition state, which 
>> also worked in this particular case. Howeve, I would also like to try our 
>> the dimer method for the purpose of re-optimising a transition state 
>> structure. To this end, I have composed an input, however, the job crashes 
>> and I keep getting an error message about certain line Search type not 
>> being implemented (looks quite obvious from the message). However, I can't 
>> seem to find what I need to change to make it work. Your advice would be 
>> much appreciated. The motion section can be found below, full input file 
>> also uploaded. 
>>
>> Any ideas on how to correctly set up a calculation using the dimer method 
>> are welcome
>>
>>
>> Thanks for your help
>>
>> Tobias
>>
>>
>>  ************************************************************************
>>  *** 16:48:48 ERRORL2 in cg_utils:cg_linmin processor 0  :: err=-1000 ***
>>  *** UNIMPLEMENTED, Line Search type not yet implemented in CG for TS ***
>>  *** search.                                                          ***
>>  ************************************************************************
>>
>>
>>  ===== Routine Calling Stack =====
>>
>>            10 cg_linmin
>>             9 cp_cg_main
>>             8 geoopt_cg
>>             7 cp_rot_opt
>>             6 cp_eval_at_ts
>>             5 cp_eval_at
>>             4 cp_cg_main
>>             3 geoopt_cg
>>             2 cp_geo_opt
>>             1 CP2K
>>
>>
>>
>>
>> &MOTION
>>   &GEO_OPT
>>     TYPE TRANSITION_STATE
>>      &TRANSITION_STATE
>>        METHOD DIMER
>>         &DIMER
>>         &ROT_OPT
>>           OPTIMIZER CG
>>         &END ROT_OPT
>>        &END DIMER
>>      &END TRANSITION_STATE
>>     OPTIMIZER CG
>>     MAX_FORCE 8.0E-4
>>     MAX_ITER 500
>>   &END GEO_OPT
>>   &PRINT
>>      &TRAJECTORY
>>       &EACH
>>          GEO_OPT 1
>>       &END EACH
>>     &END TRAJECTORY
>>   &END
>> &END MOTION
>>
>>
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