[QE-users] NEB: Atoms do not get relaxed
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Thu Apr 27 20:59:25 CEST 2023
Unsettling indeed! :-)
But happy to hear that everything is settled now.
Best
Giuseppe
Ari P Seitsonen <Ari-Paavo.Seitsonen at cnrs.fr> ha scritto:
> I think that I found it: Switching the 'restart_mode' from 'restart'
> to 'from_scratch' in the name list '&control' "released" the atoms
> to relax properly.
>
> I have no idea why this should have an effect on the relaxation: I
> always keep it as 'restart' in the calculations with the NEB, and
> the code 'pw.x' performs the restart if the files needed for a
> restart are present, otherwise the calculation starts from the given
> configuration and with the same initialisation of the electronic
> structure as with 'from_scratch', so I was expecting the same to
> happen with the NEB. My mistake, "never expect the logic of the
> developer to be the same as your own". Now happily computing all
> kinds of barriers and paths! :)
>
> Greetings from Paris and Grazie a Giuseppe again,
>
> apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
> Слава Україні
>
>
> On Thu, 27 Apr 2023, Ari P Seitsonen wrote:
>
>>
>> Dear Giuseppe,
>>
>> Thank you for the comment. One of my concerns was that the energy
>> in the images does not really change:
>>
>> grep -w ' 4 ' neb.out
>> 4 -78481.6171806 29.739170 F
>> 4 -78481.6171811 29.738137 F
>> 4 -78481.6171811 29.736993 F
>> 4 -78481.6171811 29.734436 F
>> 4 -78481.6171812 29.727381 F
>> 4 -78481.6171809 29.718296 F
>> 4 -78481.6171808 29.712880 F
>> 4 -78481.6171810 29.713046 F
>> 4 -78481.6171810 29.719086 F
>> 4 -78481.6171811 29.729326 F
>> 4 -78481.6171812 29.740800 F
>> 4 -78481.6171805 29.752151 F
>> 4 -78481.6171812 29.761356 F
>> 4 -78481.6171812 29.769083 F
>> 4 -78481.6171805 29.774024 F
>> 4 -78481.6171812 29.776518 F
>> 4 -78481.6171800 29.776688 F
>> 4 -78481.6171811 29.773882 F
>>
>> There are forces on the atoms, here again on one of them on the
>> fourth image:
>>
>> atom 84 type 2 force = -0.00407872 0.00078289 -0.00018719
>> atom 84 type 2 force = -0.00407494 0.00078224 -0.00018711
>> atom 84 type 2 force = -0.00407554 0.00078237 -0.00018713
>> atom 84 type 2 force = -0.00407560 0.00078248 -0.00018709
>> atom 84 type 2 force = -0.00407511 0.00078229 -0.00018712
>> atom 84 type 2 force = -0.00407619 0.00078255 -0.00018726
>> atom 84 type 2 force = -0.00407623 0.00078272 -0.00018718
>> atom 84 type 2 force = -0.00407528 0.00078225 -0.00018721
>> atom 84 type 2 force = -0.00407564 0.00078257 -0.00018705
>> atom 84 type 2 force = -0.00407500 0.00078222 -0.00018713
>> atom 84 type 2 force = -0.00407577 0.00078249 -0.00018711
>> atom 84 type 2 force = -0.00406905 0.00078120 -0.00018643
>> atom 84 type 2 force = -0.00407551 0.00078243 -0.00018722
>> atom 84 type 2 force = -0.00407271 0.00078203 -0.00018711
>> atom 84 type 2 force = -0.00407796 0.00078294 -0.00018727
>> atom 84 type 2 force = -0.00407607 0.00078266 -0.00018716
>> atom 84 type 2 force = -0.00407437 0.00078207 -0.00018715
>> atom 84 type 2 force = -0.00407642 0.00078274 -0.00018719
>>
>> The 'path length' indeed keeps on increasing - what is this, if the
>> energies of the images remain the same?
>>
>> initial path length = 5.0000 bohr
>> path length = 5.000 bohr
>> path length = 5.000 bohr
>> path length = 5.003 bohr
>> path length = 5.013 bohr
>> path length = 5.094 bohr
>> path length = 5.337 bohr
>> path length = 5.702 bohr
>> path length = 6.163 bohr
>> path length = 6.695 bohr
>> path length = 7.277 bohr
>> path length = 7.897 bohr
>> path length = 8.546 bohr
>> path length = 9.216 bohr
>> path length = 9.904 bohr
>> path length = 10.606 bohr
>> path length = 11.321 bohr
>> path length = 12.047 bohr
>> path length = 12.783 bohr
>>
>> Probably I am doing something really stupid somewhere... I will try
>> to look at the source code next and try to understand somewhat
>> better for what is done in the code, the meaning of the variables
>> and so on.
>>
>> Greetings,
>>
>> apsi
>>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>> Слава Україні
>>
>>
>> On Thu, 27 Apr 2023, Giuseppe Mattioli wrote:
>>
>>>
>>> Dear Ari
>>> The NEB is not exactly "stuck"
>>>
>>>> path length = 8.546 bohr
>>>> path length = 9.216 bohr
>>>> path length = 9.904 bohr
>>>
>>> The MEP length keeps increasing. Maybe a look into the trajectory
>>> files can tell you what's happening. If any other source of
>>> misbehavior can be excluded, try to go ahead (maybe fixing the
>>> position of "useless" atoms). I've experienced NEB in large
>>> systems converged after several hundreds steps.
>>> HTH
>>> Giuseppe
>>>
>>> Quoting Ari P Seitsonen <Ari-Paavo.Seitsonen at cnrs.fr>:
>>>
>>>> Dear Users,
>>>>
>>>> I have a problem in the calculations with the method NEB: The
>>>> atoms do not get relaxed even if there are clearly forces on the
>>>> atoms. The electronic structure converges well, and the
>>>> relaxation of the ions follows nicely when the NEB is not used.
>>>>
>>>> I have in the input
>>>>
>>>> BEGIN
>>>> BEGIN_PATH_INPUT
>>>> &PATH
>>>> restart_mode = 'restart'
>>>> string_method = 'neb'
>>>> nstep_path = 30
>>>> ds = 0.2
>>>> opt_scheme = "broyden"
>>>> num_of_images = 8
>>>> k_max = 0.3
>>>> k_min = 0.2
>>>> CI_scheme = "auto"
>>>> ! minimum_image = .true.
>>>> first_last_opt = .true.
>>>> path_thr = 0.1
>>>> /
>>>> END_PATH_INPUT
>>>>
>>>> and
>>>>
>>>> &ions
>>>> /
>>>>
>>>> I have tried with different values of 'num_of_images', 'k_min'
>>>> and 'k_max', with the climbing image and without. One calculation
>>>> - a diffusion path of one ad-atom on a surface - worked well, all
>>>> other become stuck with the output like:
>>>>
>>>>
>>>> ------------------------------ iteration 12
>>>> ------------------------------
>>>>
>>>> cpu = 0 tcpu = 9589.5 self-consistency for image 1
>>>> cpu = 0 tcpu = 9656.9 self-consistency for image 3
>>>> cpu = 0 tcpu = 9823.9 self-consistency for image 5
>>>> cpu = 0 tcpu = 10043.8 self-consistency for image 7
>>>>
>>>> activation energy (->) = 10.012055 eV
>>>> activation energy (<-) = 6.833374 eV
>>>>
>>>> image energy (eV) error (eV/A) frozen
>>>>
>>>> 1 -78491.5920678 0.000987 F
>>>> 2 -78490.3334035 7.018378 F
>>>> 3 -78486.4101831 18.058881 F
>>>> 4 -78481.6171805 29.752151 F
>>>> 5 -78481.5800131 29.996389 F
>>>> 6 -78485.0169815 13.489042 F
>>>> 7 -78487.7020649 7.675245 F
>>>> 8 -78488.4133872 8.072137 F
>>>>
>>>> climbing image = 5
>>>>
>>>> path length = 8.546 bohr
>>>> inter-image distance = 1.221 bohr
>>>>
>>>> ------------------------------ iteration 13
>>>> ------------------------------
>>>>
>>>> cpu = 0 tcpu = 10165.0 self-consistency for image 1
>>>> cpu = 0 tcpu = 10267.1 self-consistency for image 3
>>>> cpu = 0 tcpu = 10487.8 self-consistency for image 5
>>>> cpu = 0 tcpu = 10710.2 self-consistency for image 7
>>>>
>>>> activation energy (->) = 10.011390 eV
>>>> activation energy (<-) = 6.833374 eV
>>>>
>>>> image energy (eV) error (eV/A) frozen
>>>>
>>>> 1 -78491.5914028 0.000493 F
>>>> 2 -78490.3334036 7.099250 F
>>>> 3 -78486.4101837 17.820470 F
>>>> 4 -78481.6171812 29.761356 F
>>>> 5 -78481.5800130 29.998875 F
>>>> 6 -78485.0169810 13.636010 F
>>>> 7 -78487.7020648 7.675132 F
>>>> 8 -78488.4133870 8.071850 F
>>>>
>>>> climbing image = 5
>>>>
>>>> path length = 9.216 bohr
>>>> inter-image distance = 1.317 bohr
>>>>
>>>> ------------------------------ iteration 14
>>>> ------------------------------
>>>>
>>>> cpu = 0 tcpu = 10843.3 self-consistency for image 1
>>>> cpu = 0 tcpu = 10962.6 self-consistency for image 3
>>>> cpu = 0 tcpu = 11183.6 self-consistency for image 5
>>>> cpu = 0 tcpu = 11420.4 self-consistency for image 7
>>>>
>>>> activation energy (->) = 10.011390 eV
>>>> activation energy (<-) = 6.833374 eV
>>>>
>>>> image energy (eV) error (eV/A) frozen
>>>>
>>>> 1 -78491.5914032 0.000582 F
>>>> 2 -78490.3334034 7.139704 F
>>>> 3 -78486.4101836 17.548234 F
>>>> 4 -78481.6171812 29.769083 F
>>>> 5 -78481.5800132 29.998295 F
>>>> 6 -78485.0169814 13.849319 F
>>>> 7 -78487.7020642 7.669197 F
>>>> 8 -78488.4133871 8.072137 F
>>>>
>>>> climbing image = 5
>>>>
>>>> path length = 9.904 bohr
>>>> inter-image distance = 1.415 bohr
>>>>
>>>> ------------------------------ iteration 15
>>>> ------------------------------
>>>>
>>>> ...
>>>>
>>>> So the atoms do not move, the electronic structure is converged
>>>> in few iterations, but the energies of individual images change
>>>> in the micro-eVs.
>>>>
>>>> Any idea would be appreciated; thank you in advance for any hints.
>>>>
>>>> Greetings,
>>>>
>>>> apsi
>>>>
>>>>
>>>
>>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>>>> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>>>> Слава Україні
>>>
>>>
>>>
>>> GIUSEPPE MATTIOLI
>>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>>> Via Salaria Km 29,300 - C.P. 10
>>> I-00015 - Monterotondo Scalo (RM)
>>> Mob (*preferred*) +39 373 7305625
>>> Tel + 39 06 90672342 - Fax +39 06 90672316
>>> E-mail: <giuseppe.mattioli at ism.cnr.it>
>>>
>>> _______________________________________________
>>> The Quantum ESPRESSO community stands by the Ukrainian
>>> people and expresses its concerns about the devastating
>>> effects that the Russian military offensive has on their
>>> country and on the free and peaceful scientific, cultural,
>>> and economic cooperation amongst peoples
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
More information about the users
mailing list