[CP2K-user] [CP2K:17234] Re: Problem with 2nd generation CPMD
Onofrio Tau
onofriotau at gmail.com
Mon Jun 27 16:43:34 UTC 2022
Dear Marcella,
your suggestions were so useful! I was able to reduce to 3-4 iterations per
MD step. Sorry for my late reply but I played a lot with GAMMA and
NOISE_GAMMA to equilibrate the MD run by monitoring the temperature per
each kind. However, I have gathered some unusual behaviour (following
attached files represent *Temp per kind vs MD steps*):
1. I first assumed GAMMA 0.001 fs^-1 (value typically used in other works)
and gave different NOISE_GAMMA values for each &DEFINE_REGION (region1: Cu
slab ; region2: one toluene molecule). In all cases, for the first 100 MD
steps the temperature rapidly drops to very lower values (see attached*
gamma0.001.png* file as an example), though it partially riequilibrates to
the target T (900 K) only for sufficiently larger NOISE_GAMMA. Must be the
initial temperature drop avoided or is it sufficient only adjusting the
NOISE_GAMMA to larger values for T compensation (thus fixing GAMMA to
0.001)?
2. To avoid initial temperature drops, I have tried to directly increase
GAMMA. For 0.1 fs^-1 it seems to work well (attached *gamma0.1.png* file),
but it acts like an 'aggressive' thermostat producing large T fluctuations,
especially for the toluene region (similar situations for GAMMA = 0.01
fs^-1, attached *gamma0.01.png* file). I'm aware of the few degrees of
freedom of the single toluene molecule causing large temperature
fluctuations; therefore it is better to assume GAMMA 0.001, is it?
3. Most important: the number of iterations per MD step costantly increase
from 3-4 to 13-16 iterations during MD runs as it can be seen in the
attached output file taken as an example (*Cu_toluene.out*) with
*grep 'SCF run' Cu_toluene.out*
To restore the convergence with 3-4 iterations per MD step I sometimes did
external EXIT and then restart the run with .RESTART.wfn. It initially
works, but then the number of iterations increases again.
Is it a normal behaviour or is it due to a bad instability of the Langevin
dynamics? How to eventually avoid it?
Many thanks!
N.B.: *No* external thermostat and no velocity rescaling (TEMP_TOL) were
used during simulations.
Onofrio
Il giorno giovedì 16 giugno 2022 alle 12:23:19 UTC+2 Marcella Iannuzzi ha
scritto:
>
>
> As you may have read in previous works, to run SGCPMD a preliminary study
> is needed to set the proper GAMMA and NOISY_GAMMA parameters, which allow
> for the conservation of energy, for a Gaussian distribution of the error in
> the forces, and for a correct equipartition of the kinetic energy among the
> degrees of freedom.
> Moreover the parameters to tune the convergence of the electronic
> structure at each MD step need also to be properly adjusted to the system.
> This means that a series of preliminary simulations are needed, before the
> production runs are started.
>
> This said, my suggestions are the following:
> - Always start sgcpmd from a well converged wfn obtained along a standard
> BOMD run with diagonalisation and smearing
> - Let the first steps run on many scf iterations if needed, i.e., set
> MAX_SCF large enough
> - But use a relative large eps_scf. The wfn is not going to be optimised
> as in the BOMD, energy convergence around 10^-5 is desirable
> - Use FULL_ALL preconditioner + ASPC
> - Use a small time step
> - Tune properly GAMMA and NOISY_GAMMA
> - Monitor the conservation of energy and the temperature per kind or per
> region : TEMP_KIND
>
> Regards
> Marcella
>
> On Thursday, June 16, 2022 at 10:53:53 AM UTC+2 onofr... at gmail.com wrote:
>
>> Hi Sam,
>> yes, of course. I set up more standard BOMD with ENSEMBLE NVT and
>> DIAGONALIZATION with smear (look at my input file) and worked fine: it took
>> more or less *30 steps to reach convergence* every AIMD step.
>>
>> Then, I tried with ENSEMBLE NVT and OT (without smear obviously) and I
>> got (MAX_SCF 200):
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> * *** WARNING in qs_scf.F:598 :: SCF run NOT converged *** *** WARNING in
>> qs_scf.F:598 :: SCF run NOT converged *** *** SCF run converged in 79
>> steps *** *** SCF run converged in 72 steps *** *** SCF run converged
>> in 84 steps *** *** SCF run converged in 53 steps *** *** SCF run
>> converged in 49 steps *** *** SCF run converged in 48 steps *** ***
>> SCF run converged in 38 steps *** *** SCF run converged in 40 steps
>> *** *** SCF run converged in 38 steps *** *** SCF run converged in
>> 30 steps *** *** SCF run converged in 23 steps *** *** SCF run
>> converged in 26 steps *** *** SCF run converged in 27 steps *** ***
>> SCF run converged in 26 steps *** *** SCF run converged in 26 steps
>> *** *** SCF run converged in 23 steps *** *** SCF run converged in
>> 16 steps *** *** SCF run converged in 16 steps *** *** SCF run
>> converged in 16 steps *** *** SCF run converged in 18 steps ****
>> * ...*
>>
>> Though SCF run not converged for the first two AIMD steps, then it worked
>> sometimes fine (SCF run converged in 16 steps, but not always!). Could be a
>> possible solution.
>> N.B.: setting MAX_SCF below 200 (i.e., 50) makes SCF run not converged
>> more than two initial AIMD steps.
>>
>> Anyway, I'm looking for correctly set up SGCPMD as that found in the
>> following works:
>> - Lan, Jinggang, Jürg Hutter, and Marcella Iannuzzi. "First-principles
>> simulations of an aqueous CO/Pt (111) interface." *The Journal of
>> Physical Chemistry C* 122.42 (2018): 24068-24076.
>> - Musso, Tiziana, et al. "Second generation Car-Parrinello MD:
>> application to the h-BN/Rh (111) nanomesh." *The European Physical
>> Journal B* 91.7 (2018): 1-8.
>>
>> However, I'm struggling with and I kindly need your help.
>> Kind regards.
>>
>> Onofrio
>>
>> Il giorno giovedì 16 giugno 2022 alle 09:58:41 UTC+2 wave... at gmail.com
>> ha scritto:
>>
>>> Hi Onofrio
>>>
>>> Question: have you set this up and run a more standard simulation to
>>> work out the convergence first?
>>>
>>> If I guess, it's probably Cu as a transition metal with d-orbitals that
>>> is difficult (I am suffering with Au).
>>>
>>> Kind Regards
>>>
>>> Sam
>>> On Wednesday, June 15, 2022 at 3:20:20 PM UTC+2 onofr... at gmail.com
>>> wrote:
>>>
>>>> Dear CP2K community,
>>>>
>>>> I'm new to CP2K and I'm trying to set up a second-generation
>>>> Car-Parrinello (SGCP) MD simulation. I have started with a geometrically
>>>> optimized system of toluene adsorbed on a 3-layer Cu slab (8x6). I would to
>>>> know what sections/keywords in the input file must be used to correctly set
>>>> up a SGCPMD simulation and, possibly, the best settings to improve the
>>>> speed of such simulations since I have not found any related tutorial (but
>>>> only few things in the cp2k google group).
>>>> If I well understood, it has to be turn on the Langevin dynamics
>>>> section in combination with the OT method. For example:
>>>>
>>>> &FORCE_EVAL
>>>> ...
>>>> &DFT
>>>> ...
>>>> &QS
>>>> METHOD GPW
>>>> EXTRAPOLATION ASPC
>>>> EXTRAPOLATION_ORDER 3
>>>> EPS_DEFAULT 1.0E-10
>>>> &END QS
>>>> ...
>>>> &SCF
>>>> ...
>>>> &OT
>>>> PRECONDITIONER FULL_SINGLE_INVERSE ! or FULL_KINETIC
>>>> MINIMIZER DIIS
>>>> N_DIIS 7
>>>> &END OT
>>>> &OUTER_SCF
>>>> MAX_SCF 3
>>>> EPS_SCF 1.0E-05
>>>> &END OUTER_SCF
>>>> ...
>>>> &END SCF
>>>> ...
>>>> &END DFT
>>>> ...
>>>> &END FORCE_EVAL
>>>>
>>>> &MOTION
>>>> &MD
>>>> ENSEMBLE LANGEVIN
>>>> ...
>>>> &LANGEVIN
>>>> GAMMA 0.001
>>>> &END LANGEVIN
>>>> ...
>>>> &END MD
>>>> ...
>>>> &END MOTION
>>>>
>>>> Is it correct? To follow what I just mentioned, I prepared an input
>>>> file (attached below) based on sections/keywords defined just above and I
>>>> got from the output file (attached below) only
>>>> *"Leaving inner SCF loop after reaching 200 steps" *
>>>> (200 steps because I set MAX_SCF 200)
>>>> resulting in a very bad convergence.
>>>> As a result, it seems that I have not been running any SGCPMD
>>>> simulation but a simple bad BOMD. Am I missing something?
>>>> How can I correctly set up my input file for SGCPMD?
>>>>
>>>> Any help would be greatly appreciated.
>>>> Thanks.
>>>>
>>>> Onofrio
>>>>
>>>
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/13be0d19-e19e-4a67-8612-6f41190c6682n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220627/fee13d85/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Cu_toluene.out
Type: application/octet-stream
Size: 2734933 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220627/fee13d85/attachment-0001.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gamma0.01.png
Type: image/png
Size: 778485 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220627/fee13d85/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Cu_toluene.inp
Type: chemical/x-gamess-input
Size: 11365 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220627/fee13d85/attachment-0001.inp>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gamma0.1.png
Type: image/png
Size: 633535 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220627/fee13d85/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gamma0.001.png
Type: image/png
Size: 494605 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220627/fee13d85/attachment-0005.png>
More information about the CP2K-user
mailing list