[QE-users] [Webinar] The many roles of computational assistance and AI in the discovery of new molecules

[Minkyu Park]

Dear colleagues, this is Minkyu Park from Virtual Lab.
I delight to announce that have interesting webinar with *Prof. Connor W.
Coley from MIT* on Materials Square.
Please feel free to join & discuss more details!

*Title : *
The many roles of computational assistance and AI in the discovery of new
molecules

*Date/Time : *
Feb 6th, 2024 (22:00 ~ 23:00, KST)
Feb 6th, 2024 (14:00 ~ 15:00, CET)
Feb 6th, 2024 (08:00 ~ 09:00, EST)

*Registration :*
https://www.materialssquare.com/webinar

*Abstract : *
The identification and synthesis of molecules that exhibit a desired
function is an essential part of addressing contemporary problems in
science and technology. Small molecules are the predominant solution to
challenges in the development of medicines, chemical probes, specialty
polymers, and organocatalysts, among others. The typical discovery paradigm
is an iterative process of designing candidate compounds, synthesizing
those compounds, and testing their performance experimentally, where each
repeat of this cycle can require weeks or months. There are a variety of
techniques used for prioritizing experiments based on the predicted
property profiles of molecules. We will talk about some of the complexities
of molecular representation learning and the limitations of graph-based
models.
We will also discuss a primary consideration of molecular design workflows:
the chemical space that comprises the search space for a molecular
screening/optimization campaign.

That is, the manner in which the search is constrained to a finite library
of molecules or, following an increasingly popular trend, the manner in
which the search navigates a virtually infinite space of molecules.
Important considerations include whether the search space is constrained or
unconstrained in terms of synthesizability (or commercial availability),
which impacts the ease of experimental validation, as well as sample
efficiency.


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*Virtual Lab Inc.*
*Minkyu Park*
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   *Scientific Research on the Cloud*

*Service*. https://www.matsq.com
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[QE-users] hp.x Error in routine cdiaghg (270): problems computing cholesky

[Simon Imanuel Rombauer]

Dear QE users,

for some time I am trying to find  suitable DFT+U+V parameters for orthorhombic 
LaVO3 band structure. I was limited with with computational resources so I 
tried to manually tune the parameters to match experimental band gab. This was 
very tedious and most calculations did not converge at all. Now I have more CPU 
cores to work with and want to use the hp.x code to calculate them using DFPT. 
I followed example 02 and 06 from the documentation, that is I first calculated 
scf of LVO using a smearing and starting mag. and then did a second scf run 
with fixed occupation and total mag. = 0. Then I split the HP calculation for 
each perturbed atom. It always ends with Error in routine  cdiaghg (270):   
problems computing cholesky, I have tried to change mixing_mode, mixing_beta, 
higher ecutwfc and ecutrho, lowered the conv_thr but nothing worked. 
(input/output files appended)

Any idea is highly appreciated, also on how to speed up calculations, it still 
seems rather slow when calculating scf. 
All the best and have a nice day

Simon Rombauer
Master Student Physics
University Augsburg
Germany

PS: I manually changed the occupation in the La PP from 5d to 4f, but even when 
I left the PP as it is and simply tried to calculate U for La-5d it crashed 
with the same error.


LVO_Hubbard.7z
Description: Binary data
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[QE-users] Hubbard U Parameters in pmw.x

[Yin-Ying Ting]

Dear Quantum Espresso Community,

I am currently working with the poormanwannier.x (pmw.x) as demonstrated
in example05 of PP. In this example, the procedure begins with a
self-consistent field (SCF) calculation without the incorporation of
Wannier functions (wf) and with very small Hubbard parameters (around
0.001). This is followed by the execution of pmw.x and a subsequent
second SCF calculation, this time including Wannier functions and the
Hubbard U parameters.

My question pertains to the rationale behind this two-step SCF
calculation approach, particularly concerning the Hubbard U parameters.
Why is it not recommended or feasible to employ the Hubbard U parameters
right from the first SCF calculation? Understanding the underlying
reasoning for this process would greatly enhance my comprehension of the
method and its applications.

I appreciate any insights or explanations you can provide. Thank you for
your time and assistance.

Best regards,

PhD student in Forschungszentrum Jülich

Yin-Ying Ting

--

Forschungszentrum Jülich GmbH
Institute of Energy and Climate Research
Theory and Computation of Energy Materials (IEK-13)
E-mail: y.t...@fz-juelich.de





Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens


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[QE-users] Issues with vc-relax for a slab

[Anupriya Nyayban]

Dear users and experts,

I have considered a (311) plane of 2 layers of ZnFe2O4 structure. The
attached input file is for the vc-relax calculation. The following is how
the energy changes after each optimization step. At the last optimization
step ( Energy error = 1.5E+00 Ry), scf didn't converge even after 300
iterations.
Energy error=  0.0E+00 Ry
 Energy error=  1.9E+01 Ry
 Energy error=  2.5E+01 Ry
 Energy error=  2.7E+01 Ry
 Energy error=  2.7E+01 Ry
 Energy error=  2.7E+01 Ry
 Energy error=  2.4E+01 Ry
 Energy error=  2.0E+01 Ry
 Energy error=  1.5E+01 Ry
 Energy error=  1.1E+01 Ry
 Energy error=  8.3E+00 Ry
 Energy error=  6.5E+00 Ry
 Energy error=  5.1E+00 Ry
 Energy error=  4.3E+00 Ry
 Energy error=  3.7E+00 Ry
 Energy error=  3.2E+00 Ry
 Energy error=  2.8E+00 Ry
 Energy error=  2.5E+00 Ry
 Energy error=  2.2E+00 Ry
 Energy error=  2.0E+00 Ry
 Energy error=  1.7E+00 Ry
 Energy error=  1.5E+00 Ry
Please suggest how I can overcome the issue and what may be the reason!

Thank you!

With regards
Anupriya Nyayban
IIT Madras, India


zn311vc.in
Description: Binary data
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Re: [QE-users] Convergence problem with hydroxide

[Giuseppe Mattioli]

Dear Jeremy
It is not a technical problem, it is a theoretical one.
negative ions in gas phase generally yield unbound excess electrons  
leading to weird results when computed at the GGA level of theory. Of  
course water stabilizes OH-, and also exact exchange if you use a  
hybrid functional.

HTH
Giuseppe

Quoting RABONE Jeremy :


Hello,

  I have just started a project using QE, and have a question  
regarding a hydroxide ion in a box. When I first tried to do a  
relaxation with conv_thr = 1.0d-8, it started off like it was going  
to converge and then suddenly the convergence went all over the  
place. Changing all of the other parameters made no difference, but  
reducing
conv_thr to 1.0d-6 stops the scf step before the problem and the  
calculation completes. There also seems to be some effect of the  
randomised starting wavefunctions even with conv_thr = 1.0d-6  
(sometimes converges, sometimes goes all triplets). When surrounding  
the ion with a water cage, the calculation works with no problems.  
If I switch to a spin polarized calculation, with conv_thr = 1.0d-8  
it seems determined to converge to a triplet state with the first  
antibonding orbital occupied, and does so with no difficulty is the  
magnetization is set to 2.


I recall there were sometimes issues in DFT when the order of state  
energies changes during a calculation - is this what is happening  
here and is there a way to get passed the problem or do I just have  
to be content with a reduced threshold ?


A S2- ion in a box does something similar - seemingly converging to  
triplet with a d-state occupied, and even when surrounded by a water  
cage it fails to converge in a singlet state (although in this case  
one might question the validity of the calculation).


I'm using SG15 norm-conserving pseudopotentials but the PAW  
pseudopotential seems to do the same thing.


Regards,

Jeremy




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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Mob (*preferred*) +39 373 7305625
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E-mail: 

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[QE-users] Convergence problem with hydroxide

[RABONE Jeremy]

Hello,

  I have just started a project using QE, and have a question regarding a 
hydroxide ion in a box. When I first tried to do a relaxation with conv_thr = 
1.0d-8, it started off like it was going to converge and then suddenly the 
convergence went all over the place. Changing all of the other parameters made 
no difference, but reducing
conv_thr to 1.0d-6 stops the scf step before the problem and the calculation 
completes. There also seems to be some effect of the randomised starting 
wavefunctions even with conv_thr = 1.0d-6 (sometimes converges, sometimes goes 
all triplets). When surrounding the ion with a water cage, the calculation 
works with no problems. If I switch to a spin polarized calculation, with 
conv_thr = 1.0d-8 it seems determined to converge to a triplet state with the 
first antibonding orbital occupied, and does so with no difficulty is the 
magnetization is set to 2.

I recall there were sometimes issues in DFT when the order of state energies 
changes during a calculation - is this what is happening here and is there a 
way to get passed the problem or do I just have to be content with a reduced 
threshold ?

A S2- ion in a box does something similar - seemingly converging to triplet 
with a d-state occupied, and even when surrounded by a water cage it fails to 
converge in a singlet state (although in this case one might question the 
validity of the calculation).

I'm using SG15 norm-conserving pseudopotentials but the PAW pseudopotential 
seems to do the same thing.

Regards,

Jeremy

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