Re: [QE-users] Magnetic Susceptibility from NMR.out (hamed asadi)

[Robert Molt]

Mr. Albuquerque,

I wanted to thank you for citing original papers. I am always trying to 
find the foundational papers, to read matters from the beginning. I love 
it when people do that on this forum.


On 9/22/20 9:03 PM, Marcelo Albuquerque wrote:

Dear Hamed,

The calculation of the susceptibility is intrinsically related to the 
chemical shift. Please, check these papers (below), and the GIPAW 
documentation.


Mauri, F., Pfrommer, B. G., & Louie, S. G. (1996). Ab initio theory of 
NMR chemical shifts in solids and liquids. /Physical review letters/, 
/77/(26), 5300.


Mauri, F., & Louie, S. G. (1996). Magnetic susceptibility of 
insulators from first principles. /Physical review letters/, /76/(22), 
4246.


I hope you figure it useful.

Best wishes.

/
/ Marcelo Albuquerque/
//
/  Ph.D. Student/
//
/ Physics Institute/
//
/Universidade Federal Fluminense (UFF)/
/
/   Niterói/RJ - Brazil/

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users


--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Which pressure should I report on my work???

[Robert Molt]

If I may ask a question to clarify a point within this thread…I have always had 
some confusion on exactly why the the # of basis vectors is not conserved 
step-to-step. This is an implicit aspect to the question being asked, if I 
understand properly.

1.) Why is the number of plane waves during vc-relax steps constant? Why is not 
held to a constant energy cutoff, like in an energy calculation? 

My understanding is that ecutrho and ecutwfc “constrain” the number of plane 
waves during a vc-relax calculation; these two variables completely specify the 
number of allowed plane waves consistent with the initial unit cell volume. Is 
this correct?

My understanding is that if you wanted a constant energy cutoff, you have to 
vary the number of plane waves, since the volume is changing. Why is this 
undesirable to do? Is it because comparing different numbers of plane waves 
results in different energies, such that no fair comparison can be made between 
calculations with different numbers of basis vectors?

2.) On this specific question asked by Mohad, I am slightly confused. Is the 
essence of the problem that the pressure calculation threshold is too low OR is 
it that you should never use the “properties” other than lattice constants from 
a vc-relax for the aforementioned reason? In my head, these are seemingly 
independent issues in how the calculations are working?

Dr. Robert Molt Jr.
Indiana University Purdue University


> On Sep 20, 2020, at 6:03 AM, Lorenzo Monacelli 
>  wrote:
> 
> If I interpret correctly the question, you are seeing a P = 6.57 kbar and not 
> 7 as in the pw.x input press keyword because, when qe relax the unit cell, it 
> constrains the basis defined with ecutwfc and ecutrho. This basis, as it is 
> formed by plane waves with periodic boundaries, depends on the cell size. So 
> the code will relax reaching 7 kbar (within the accuracy you chose in the 
> input, usually 0.1 kbar), then it will run a new calculation in the final 
> cell recomputing the basis with the new cell. So the value of the pressure 
> will be slightly different.
> 
> To be consistent, you should use 6.57 kbar in your plots, as it is the final 
> pressure with the cutoffs you used for your calculation, and does not depend 
> on the starting cell. If you want exactly 7 kbar, you can start a new 
> vc-relax using the final structure you have at 6.57 kbar as starting point, 
> and it will get to a much closer value.
> 
> Bests,
> 
> Lorenzo
> 
> Il 20/09/20 10:54, Stefano Baroni ha scritto:
>> What is difference between the frequencies computed at: i) P=0; ii) P=6.57 
>> kbar;  iii) 7 kbar? The answer to my question will imply that to yours. SB
>> 
>> — 
>> Stefano Baroni -  SISSA, Trieste - http://stefano.baroni.me 
>> <http://stefano.baroni.me/>, stefanobaroni (Skype) 
>> 
>> If the prediction that an airplane can stay up depends on the difference 
>> between Riemann and Lebesgue integration, I don’t want to fly in it [Richard 
>> W. Hammings]
>> 
>> 
>> 
>>> On 20 Sep 2020, at 10:42, Mohad Abbasnejad >> <mailto:mohaddeseh.abbasne...@gmail.com>> wrote:
>>> 
>>> Hello Dear QE users
>>> I am studying the effect of pressure on the frequencies.
>>> In the experimental article, the pressure on the solid has been reported to 
>>> be 7 kbar.
>>> 
>>> When I put this pressure (7 kbar) on my structure and let it relax, the 
>>> final pressure is calculated to be 6.57 kbar as the following. Therefore it 
>>> is not exactly 7 kbar.
>>> 
>>> Computing stress (Cartesian axis) and pressure
>>> 
>>>   total   stress  (Ry/bohr**3)   (kbar) P=
>>> 6.57
>>>0.4467   0.  -0.  6.57  0.00 -0.00
>>>0.   0.4467  -0.  0.00  6.57 -0.00
>>>   -0.  -0.   0.4467 -0.00 -0.00  6.57
>>> 
>>> 
>>> MY QUESTION: Which pressure should I report on my paper;  7 kbar or 6.57 
>>> kbar?
>>> 
>>> 
>>> Any comments would be appreciated.
>>> 
>>> Best regards
>>> Mohaddeseh
>>> 
>>> 
>>> -- 
>>> -
>>> Mohaddeseh Abbasnejad, 
>>> Assistant Professor of Physics,
>>> Faculty of Physics, 
>>> Shahid Bahonar University of Kerman,
>>> Kerman, Iran
>>> P.O. Box 76169-133
>>> Tel: +98 34 31322199
>>> Fax: +98 34 33257434
>>> Cellphone: +98 917 731 7514
>>> E-Mail: mohaddeseh.abbasne...@gmail.com 
>>&g

Re: [QE-users] Schrödinger & Kohn: A Stack Exchange for the modeling of molecules and materials

[Robert Molt]

Good evening,

I have seen this advertisement on CCL as well. I do not understand what 
the proposed "launch" is. I see the name of one of the greatest 
physicists of all time and then Kohn; what is the site/group intending 
to do?


On 4/2/20 11:56 AM, Rashid Rafeek V Valappil wrote:

Dear All,

On the 18th of April, the Stack Exchange network (which hosts 
StackOverflow, MathOverflow, and many other Q/A sites) is anticipated 
to launch a site called "Schrödinger & Kohn" in two stages. People who 
register now will be invited to participate in the first stage, during 
which the scope and future of this site is decided for 2 weeks, before 
the final launch opens universally.


More than 190 people have already signed up. If you or any of your 
group members might be interested in having a say in this community's 
scope or organization, please follow the steps below to register to 
the site:


*_1)_ *Log into Stack Exchange: https://stackexchange.com 
<https://stackexchange.com/>
*_2)_ *Visit the Stack Exchange staging zone for new sites: 
https://area51.stackexchange.com/
*_3)_* When you click "sign up" it will automatically log you in with 
your Stack Exchange credentials
*_4)_* The materials modeling site is then here: 
https://area51.stackexchange.com/proposals/122958/materials-modeling?referrer=OWJmN2MxOWQ5ZjQ5NDQ5NWFlNDRjOWYzNjNiMWRjYjAxMjA4NGE2MmUyYjQ1NDQ0NDFhYzRkMjEzZmZlNGZkNJVYNM_b97JfvwNIZroMyCql4XhhRD2FJqfkBrtTfajj0
*_5)_* Click "commit" and then you will get a verification code in 
your email.


Proposed topics so far have been related to the usage of VASP, 
QuantumEspresso, OpenMOLCAS, CFOUR, GAUSSIAN, LAMMPS, CP2K, DIRAC, 
Turbomole, MOLPRO, ORCA, MRCC, ADF, PySCF, PSI4, DALTON, QChem, 
CASTEP, CPMD, ABINT, DFTB+, ABAQUS, OpenBabel, MPQC, NWChem, MOLDEN, 
GAMMES(US), GAMMES(UK), HORTON, NECI, DICE, OpenFermion, HANDE, but 
there is still time to expand the scope to more software. If your 
group has software that is not yet represented, you may wish to have 
someone register for the 2-week staging period during which the scope 
and future of this site will be determined.


With best wishes!
Rashid Rafeek

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users


--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] differently complied QE

[Robert Molt]

Question:

You mentioned the BO as being a limitation on the accuracy of lattice 
constants. Can you cite a reference on this for reading? I was unaware 
that this was ever meaningfully a source of error in an equilibrium 
geometric property.


IUPUI

On 1/7/19 10:54 PM, Stefano Baroni wrote:

Aleksandra:

you are very right and I commend you for your thoroughness. Only 
figures that can be reproduced should be reported. Usually, lattice 
constants can be computed and reported with a higher accuracy than you 
observe. This being said, as Nicola says, the *numerical* accuracy 
that can be achieved is usually higher than needed for practical 
purposes and higher than the accuracy due to “unavoidable” physical 
approximations (first and foremost the XC functional, but also more 
fundamental ones, such as Born-Oppenheimer’s).


Coming to the point, that numerical results may depend on such 
seemingly irrelevant “details" as hardware, mathematical libraries, 
optimisation level, etc. is not uncommon, as surprising as it may 
seem, particularly on parallel machines. The result of many 
“commutative” operations (sums, products) depends in practice on the 
order in which these operations are performed, due to the 
non-commutativity fo rounding errors, and this order does depend on 
all those “details”. Some properties may be more sensitive to these 
details than others in some systems more than in others. For instance, 
structural parameters (such as lattice parameters or atomic positions) 
are more sensitive to the accuracy in stresses and forces in soft 
systems than in hard ones. Can you tell why?


Bottom line. Please, do the tests that Nicola suggests and make sure 
you understand the results you get (I am sure you are able to 
appreciate if and when you understand, which is not so common). In 
case of need, revert to us.


Good luck!
Stefano Baroni

On 8 Jan 2019, at 00:49, Aleksandra Oranskaia 
<mailto:aleksandra.oransk...@kaust.edu.sa>> wrote:


Thank you for the respond!

I was confused with the difference, because if the 3rd digit is 
“arbitrary” (depends on libraries, compilers, hardware, etc.) than 
there is no sense in reporting lattice constants in papers with this 
accuracy; however, it is a common practice.


I used:
conv_thr=1.d-8
tot_conv_thr=1.d-6
forc_conv_thr=1.d-6
cell_dofree=‘volume’ (for the cubic cell)

I will try to increase conv_thr and press_conv_thr, as well as to 
compare gnu and intel compillations, and reply back.



Best,
Alex.

___
Aleksandra Oranskaia (M.Sc.)
ChemS PhD student, KAUST
Phone: +966 50 1335254


—
Stefano Baroni -  SISSA, Trieste - http://stefano.baroni.me 
<http://stefano.baroni.me/>, stefanobaroni (Skype)


And aren’t we all tired of those who claim to know the answer to life, 
death and the creation being so […] sensitive about their knowledge? 
[Stephen Fry]







___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users


--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

[QE-users] Security Problem for Quantum Espresso Mailing List

[Robert Molt]

Sirs and Madames:

There is a significant security lapse for this list-serv. The mailing 
list monthly reminder  writes the user's password out, in the email. 
This is *not *acceptable security practice in the present day; it is not 
OK to ever have an email list out a user's password for any reason. It 
is important to not allow one compromised account (say, email) lead to 
further compromises.


I please ask that this be remedied.

--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com
IUPUI

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Local charge

[Robert Molt]

Without knowing your system, it is impossible to comment on whether the 
concept of local charge exists, meaningfully. Can you specify your system?


For example, there is no such thing as a widely-accepted method to 
calculate local charge because the concept of local charge does not 
exist, rigorously. No law of physics demands that electrons are "owned" 
by a certain atom (Coulomb's law neither knows nor cares about the human 
concept of atoms). In some cases, electrons' positions happen to be 
relatively localized (like, say average organic molecules), and the term 
has more meaning. If we are talking about a highly delocalized system, 
the term has no meaning (because the electrons don't "belong" to anyone).



On 8/11/18 3:25 PM, Comer, Benjamin M wrote:


Mr. Hosseini,

I am not sure what type the local charges and magnetizations QE prints 
by default, but you should use a widely accepted method to calculate 
local charges, such as Bader analysis. I should note that there is no 
“correct” way to calculate a local charge. However, there are many 
ways to calculate charges developed by the community, each with it’s 
own drawbacks (see Wikipedia link below.) I’d recommend using Bader 
charges, DDEC6, or the lowden charges printed out from the projwfc.x 
code in the quantum espresso suite(links below.)


https://en.wikipedia.org/wiki/Partial_charge

http://theory.cm.utexas.edu/henkelman/code/bader/

https://sourceforge.net/projects/ddec/files/

http://phya.snu.ac.kr/~nmcuong/board/physics/INPUT_PROJWFC.html 
<http://phya.snu.ac.kr/%7Enmcuong/board/physics/INPUT_PROJWFC.html>


Hope it helps,

Ben Comer

Georgia Tech

>Dear All

>

>I need to compute local charge of atoms in my unit cell. As I checked, the 
output of SCF provides local charge with the corresponding 
>magnetization. The numbers are confusing. How can I compute the local 
charge?


>

>M.R.Hosseini

>Tarbiat Modares University, Department of Chemistry, Iran



___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users


--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [Pw_forum] Namelist Error

[Robert Molt]

Good evening,

I am confused on the rules for the quotes. The below is another file I 
used for calculation (a vx-relax, which is why I left some of those 
fields for the previously posted input file), which ran just fine. In 
this one, I did not use quotes around many of the items in  and 
it ran just fine. I am certainly happy to try the suggested fixes, but I 
assumed the quotes are not necessary based on the successful execution 
of the below file?



calculation  = "vc-relax"
outdir='/p/work1/workspace/molt/Espresso_Test',
pseudo_dir = '~/Espresso_PP/',
restart_mode = "from_scratch"
/

   input_dft=pbe,
   ibrav = 1,
   celldm(1) = 7.969,
   nat = 8,
   ntyp = 2,
   nbnd = 72,
   ecutwfc = 80.0,
   occupations = 'smearing',
   smearing = 'fd',
   degauss = 0.000633363
   vdw_corr= grimme-d2
/

   diagonalization = 'david'
/

   ion_dynamics=bfgs
/

   cell_dynamics=bfgs
/
ATOMIC_SPECIES
 Mg 24.305 Mg.pbe-nsp-bpaw.UPF.txt
 O 15.999 O.pbe-n-kjpaw_psl.0.1.UPF.txt
ATOMIC_POSITIONS alat
Mg 0.0 0.0 0.0
Mg 0.0 0.5 0.5
Mg 0.5 0.0 0.5
Mg 0.5 0.5 0.0
O 0.5 0.5 0.5
O 0.5 0.0 0.0
O 0.0 0.5 0.0
O 0.0 0.0 0.5
K_POINTS automatic
   3 3 3 0 0 0


On 8/12/17 3:51 PM, Isaiah Moses wrote:

Hi Robert,
You need  only for *'vc-relax' or 'vc-md.
*
You don't need that name list for 'relax' calculation.

Regards,
Isaiah

On Sat, Aug 12, 2017 at 8:39 PM, Robert Molt 
<r.molt.chemical.phys...@gmail.com 
<mailto:r.molt.chemical.phys...@gmail.com>> wrote:


Good evening,

I am encountering an error I know not how to resolve as a namelist
error
(Error in routine  read_namelists (19):). I do not believe I lack any
commas as needed, but clearly I do not appreciate my syntax error.



 calculation  = "relax"
 outdir='/p/work1/workspace/molt/Espresso_Test',
 pseudo_dir = '~/Espresso_PP/',
 restart_mode = "from_scratch"
/

input_dft=pbe,
ibrav = 1,
celldm(1) = 26.952,
Nosym=.TRUE.,
nat = 176,
dipfield=.TRUE.,
tefield=.TRUE.,
ntyp = 3,
ecutwfc = 40.0,
occupations = 'smearing',
smearing = 'fd',
degauss = 0.000633363,
vdw_corr= grimme-d2,
assume_isolated=esm,
esm_bc=bc1
/

diagonalization = 'david'
/

ion_dynamics=bfgs
/

cell_dynamics=bfgs
/
ATOMIC_SPECIES
  Mg 24.305 Mg.pbe-nsp-bpaw.UPF.txt
  O 15.999 O.pbe-n-kjpaw_psl.0.1.UPF.txt
  H 1.008  H.pbe-kjpaw_psl.0.1.UPF.txt
ATOMIC_POSITIONS angstrom
Mg  -3.21830822499 -3.17850017999 -7.41649997501 1 1 1
Mg  -3.21830822499 -1.05950009000 -5.29750001501 1 1 1
Mg  -1.09930813500 -3.17850017999 -5.29750001501 1 1 1
Mg  -1.09930813500 -1.05950009000 -7.41649997501 1 1 1
Mg  -3.21830822499 -3.17850017999 -3.17849981500 1 1 1
Mg  -3.21830828500 -3.17850024000 5.29750002500 0 0 0
Mg  1.01969182500 -3.17850017999 -7.41649997501 1 1 1
Mg  -3.21830822499 1.05949987000 -7.41649997501 1 1 1
Mg  -3.21830822499 -1.05950009000 -1.05949985500 1 1 1
Mg  -3.21830828500 -1.05950034000 7.41649997499 0 0 0
Mg  1.01969182500 -1.05950009000 -5.29750001501 1 1 1
Mg  -3.21830822499 3.17849982000 -5.29750001501 1 1 1
Mg  -1.09930813500 -3.17850017999 -1.05949985500 1 1 1
Mg  -1.09930838500 -3.17850024000 7.41649997499 0 0 0
Mg  3.13869177500 -3.17850017999 -5.29750001501 1 1 1
Mg  -1.09930813500 1.05949987000 -5.29750001501 1 1 1
Mg  -1.09930813500 -1.05950009000 -3.17849981500 1 1 1
Mg  -1.09930838500 -1.05950034000 5.29750002500 0 0 0
Mg  3.13869177500 -1.05950009000 -7.41649997501 1 1 1
Mg  -1.09930813500 3.17849982000 -7.41649997501 1 1 1
Mg  -3.21830822499 -3.17850017999 1.05950010500 0 0 0
Mg  -3.21830822499 -1.05950009000 3.17850006500 0 0 0
Mg  -1.09930813500 -3.17850017999 3.17850006500 0 0 0
Mg  -1.09930813500 -1.05950009000 1.05950010500 0 0 0
Mg  -3.21830822499 1.05949987000 -3.17849981500 1 1 1
Mg  -3.21830828500 1.05949987000 5.29750002500 0 0 0
Mg  1.01969182500 -3.17850017999 -3.17850031500 1 

[Pw_forum] Namelist Error

[Robert Molt]

Good evening,

I am encountering an error I know not how to resolve as a namelist error 
(Error in routine  read_namelists (19):). I do not believe I lack any 
commas as needed, but clearly I do not appreciate my syntax error.



 calculation  = "relax"
 outdir='/p/work1/workspace/molt/Espresso_Test',
 pseudo_dir = '~/Espresso_PP/',
 restart_mode = "from_scratch"
/

input_dft=pbe,
ibrav = 1,
celldm(1) = 26.952,
Nosym=.TRUE.,
nat = 176,
dipfield=.TRUE.,
tefield=.TRUE.,
ntyp = 3,
ecutwfc = 40.0,
occupations = 'smearing',
smearing = 'fd',
degauss = 0.000633363,
vdw_corr= grimme-d2,
assume_isolated=esm,
esm_bc=bc1
/

diagonalization = 'david'
/

ion_dynamics=bfgs
/

cell_dynamics=bfgs
/
ATOMIC_SPECIES
  Mg 24.305 Mg.pbe-nsp-bpaw.UPF.txt
  O 15.999 O.pbe-n-kjpaw_psl.0.1.UPF.txt
  H 1.008  H.pbe-kjpaw_psl.0.1.UPF.txt
ATOMIC_POSITIONS angstrom
Mg  -3.21830822499 -3.17850017999 -7.41649997501 1 1 1
Mg  -3.21830822499 -1.05950009000 -5.29750001501 1 1 1
Mg  -1.09930813500 -3.17850017999 -5.29750001501 1 1 1
Mg  -1.09930813500 -1.05950009000 -7.41649997501 1 1 1
Mg  -3.21830822499 -3.17850017999 -3.17849981500 1 1 1
Mg  -3.21830828500 -3.17850024000 5.29750002500 0 0 0
Mg  1.01969182500 -3.17850017999 -7.41649997501 1 1 1
Mg  -3.21830822499 1.05949987000 -7.41649997501 1 1 1
Mg  -3.21830822499 -1.05950009000 -1.05949985500 1 1 1
Mg  -3.21830828500 -1.05950034000 7.41649997499 0 0 0
Mg  1.01969182500 -1.05950009000 -5.29750001501 1 1 1
Mg  -3.21830822499 3.17849982000 -5.29750001501 1 1 1
Mg  -1.09930813500 -3.17850017999 -1.05949985500 1 1 1
Mg  -1.09930838500 -3.17850024000 7.41649997499 0 0 0
Mg  3.13869177500 -3.17850017999 -5.29750001501 1 1 1
Mg  -1.09930813500 1.05949987000 -5.29750001501 1 1 1
Mg  -1.09930813500 -1.05950009000 -3.17849981500 1 1 1
Mg  -1.09930838500 -1.05950034000 5.29750002500 0 0 0
Mg  3.13869177500 -1.05950009000 -7.41649997501 1 1 1
Mg  -1.09930813500 3.17849982000 -7.41649997501 1 1 1
Mg  -3.21830822499 -3.17850017999 1.05950010500 0 0 0
Mg  -3.21830822499 -1.05950009000 3.17850006500 0 0 0
Mg  -1.09930813500 -3.17850017999 3.17850006500 0 0 0
Mg  -1.09930813500 -1.05950009000 1.05950010500 0 0 0
Mg  -3.21830822499 1.05949987000 -3.17849981500 1 1 1
Mg  -3.21830828500 1.05949987000 5.29750002500 0 0 0
Mg  1.01969182500 -3.17850017999 -3.17850031500 1 1 1
Mg  1.01969182500 -3.17850024000 5.29750002500 0 0 0
Mg  1.01969182500 1.05949987000 -7.41649997501 1 1 1
Mg  -3.21830822499 3.17849982000 -1.05949985500 1 1 1
Mg  -3.21830828500 3.17849982000 7.41649997499 0 0 0
Mg  1.01969182500 -1.05950009000 -1.05950035501 1 1 1
Mg  1.01969182500 -1.05950034000 7.41649997499 0 0 0
Mg  1.01969182500 3.17849982000 -5.29750001501 1 1 1
Mg  -1.09930813500 1.05949987000 -1.05949985500 1 1 1
Mg  -1.09930838500 1.05949987000 7.41649997499 0 0 0
Mg  3.13869177500 -3.17850017999 -1.05950035501 1 1 1
Mg  3.13869177500 -3.17850024000 7.41649997499 0 0 0
Mg  3.13869177500 1.05949987000 -5.29750001501 1 1 1
Mg  -1.09930813500 3.17849982000 -3.17849981500 1 1 1
Mg  -1.09930838500 3.17849982000 5.29750002500 0 0 0
Mg  3.13869177500 -1.05950009000 -3.17850031500 1 1 1
Mg  3.13869177500 -1.05950034000 5.29750002500 0 0 0
Mg  3.13869177500 3.17849982000 -7.41649997501 1 1 1
Mg  -3.21830822499 1.05949987000 1.05950010500 0 0 0
Mg  1.01969182500 -3.17850017999 1.05950010500 0 0 0
Mg  -3.21830822499 3.17849982000 3.17850006500 0 0 0
Mg  1.01969182500 -1.05950009000 3.17850006500 0 0 0
Mg  -1.09930813500 1.05949987000 3.17850006500 0 0 0
Mg  3.13869177500 -3.17850017999 3.17850006500 0 0 0
Mg  -1.09930813500 3.17849982000 1.05950010500 0 0 0
Mg  3.13869177500 -1.05950009000 1.05950010500 0 0 0
Mg  1.01969182500 1.05949987000 -3.17849981500 1 1 1
Mg  1.01969182500 1.05949987000 5.29750002500 0 0 0
Mg  1.01969182500 3.17849982000 -1.05949985500 1 1 1
Mg  1.01969182500 3.17849982000 7.41649997499 0 0 0
Mg  3.13869177500 1.05949987000 -1.05949985500 1 1 1
Mg  3.13869177500 1.05949987000 7.41649997499 0 0 0
Mg  

Re: [Pw_forum] "Centering" Requirement of ESM

[Robert Molt]

I appreciate the help. If ESM does not require this symmetry, can you 
explain what is meant by the manual's statement of:


:

"Requires cell with a_3 lattice vector along z,

normal to the xy plane, with the slab centered around z=0. Also requires 
symmetry checking to be
 disabled along z, either by settingnosym 
<http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nosym>  = .TRUE.

 or by very slight displacement (i.e., 5e-4 a.u.)
 of the slab along z."


I want to make sure I am in compliance with the manual's specifications, 
and I clearly must not understand what that means if I misinterpreted it 
to mean it requires symmetry along the z axis.



Separately, given that we have no symmetry in xy, is it logically 
necessary to "cap" boundary atoms with hydrogens (or the like) to avoid 
artifacts at the boundary?



On 7/28/17 6:41 PM, 大谷実 wrote:

Dear Robert,

Besides Lorenzo’s message, I can add one more thing. ESM does not 
require symmetry along z-axis, so you do not need to put an additional 
adsorbate molecule on the bottom.



Also requires symmetry checking to be
  disabled along z, either by settingnosym

<http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nosym>  = 
.TRUE.
  or by very slight displacement (i.e., 5e-4 a.u.)
  of the slab along z.




Best regard,
Minoru

Minoru Otani
National Institute of Advanced Industrial Science and Technology
Research Centre for Computational Design of Advanced Functional Materials
email : minoru.ot...@aist.go.jp <mailto:minoru.ot...@aist.go.jp>
-

On Jul 29, 2017, at 5:15, Lorenzo Paulatto 
<lorenzo.paula...@impmc.upmc.fr> wrote:


It does not matter, it is only need to be roughly centered

--
Lorenzo Paulatto
Written on a virtual keyboard with real fingers

On 28 Jul 2017 9:36 p.m., "Dr. Robert Molt Jr." 
<r.molt.chemical.phys...@gmail.com 
<mailto:r.molt.chemical.phys...@gmail.com>> wrote:


Good evening,

I am confused by the "centering" requirements of ESM. It is
stated that:

Requires cell with a_3 lattice vector along z,
  normal to the xy plane, with the slab centered
  around z=0. Also requires symmetry checking to be
  disabled along z, either by settingnosym

<http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nosym>  = 
.TRUE.
  or by very slight displacement (i.e., 5e-4 a.u.)
  of the slab along z.

I have constructed a slab which is symmetric about the xy plane
and centered around z=0 contour. This is fine and good.

However, once I add the adsorbate molecule, I cannot have
symmetry...unless it is intended that I add the same adsorbate
molecule on the "bottom" of the simulation, too? I am unclear
what is meant by the slab being "centered." Center of mass?
Center of symmetry?



___
Pw_forum mailing list
Pw_forum@pwscf.org <mailto:Pw_forum@pwscf.org>
http://pwscf.org/mailman/listinfo/pw_forum
<http://pwscf.org/mailman/listinfo/pw_forum>

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Lattice Constant of ESM Slab

[Dr. Robert Molt Jr.]

Addendum:

Below, you noted that periodicity only exists along z-hat in an ESM 
calculation. Would a corollary therein be that one needs to "cap" 
boundary atoms along the xz and yz planes with hydrogens (or the like) 
to fulfill the octets that would otherwise be satisfied by PBCs in those 
directions?


On 7/28/2017 12:23 PM, naz...@iasbs.ac.ir wrote:
>   celldm(1)=10+4a
>
>   this is correct. Remember put the 2*2*4 unit cell in the midl of cube
>   with dimension 10+4a. (..5.(4a)a...5).
>
>
>   regards
>Fariba
>   IASBS
>
>
>
>> To be explicit, is this correct:
>>
>> celldm(1)=10+4a
>>
>> if it's a 2x2x4 slab, z height is 4a? Or is it
>>
>> celldm(1)=10+2a
>>
>> because the program requires/assumes that there is symmetry in the xy
>> plane for z=0, and has already factored that in?
>>
>> On 7/28/2017 11:53 AM, naz...@iasbs.ac.ir wrote:
>>> Hi,
>>>
>>>in slab model periodicity is restricted in one dimension, Suppose Z.
>>>
>>>in your example you should fit the cube with a dimension in the cube
>>> with
>>>
>>>a+10 dimension.(-...10/2..a.10/2..)
>>>
>>>
>>>I do hope this help
>>>
>>> regards
>>> Fariba
>>> IASBS
>>>
>>>
>>>
>>>
>>>> Good afternoon,
>>>>
>>>> I do not understand how the lattice constant is defined in an ESM
>>>> calculation of a slab.
>>>>
>>>> Let's say I have a 2x2x4 slab, and wish to simulate a vacuum on either
>>>> side of it. Let us say the unit cells are simple cubic, such that the
>>>> height is "a". For a 10 Angstrom vacuum, I assume L/2=10, pursuant to
>>>> the diagram on
>>>> (http://sugino.issp.u-tokyo.ac.jp/esm/index.php?SIESTA%2BESM%20Manual).
>>>> If I do
>>>>
>>>> assume_isolated=esm
>>>>
>>>> esm_bc=bc1
>>>>
>>>> Is the lattice constant for this situation defined as
>>>>
>>>> celldm(1)= L/2 + 4a + L/2
>>>>
>>>> ?
>>>>
>>>> Dr. Robert Molt
>>>>
>>>> Indiana University Perdue University
>>>>
>>>> ___
>>>> Pw_forum mailing list
>>>> Pw_forum@pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>> --
>>>> This message has been scanned for viruses and
>>>> dangerous content by MailScanner, and is
>>>> believed to be clean.
>>>>
>>>>
>>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>
>

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] "Centering" Requirement of ESM

[Dr. Robert Molt Jr.]

Good evening,

I am confused by the "centering" requirements of ESM. It is stated that:

Requires cell with a_3 lattice vector along z,
 normal to the xy plane, with the slab centered
 around z=0. Also requires symmetry checking to be
 disabled along z, either by settingnosym 
  = .TRUE.

 or by very slight displacement (i.e., 5e-4 a.u.)
 of the slab along z.

I have constructed a slab which is symmetric about the xy plane and 
centered around z=0 contour. This is fine and good.


However, once I add the adsorbate molecule, I cannot have 
symmetry...unless it is intended that I add the same adsorbate molecule 
on the "bottom" of the simulation, too? I am unclear what is meant by 
the slab being "centered." Center of mass? Center of symmetry?



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Lattice Constant of ESM Slab

[Dr. Robert Molt Jr.]

Good afternoon,

I do not understand how the lattice constant is defined in an ESM 
calculation of a slab.

Let's say I have a 2x2x4 slab, and wish to simulate a vacuum on either 
side of it. Let us say the unit cells are simple cubic, such that the 
height is "a". For a 10 Angstrom vacuum, I assume L/2=10, pursuant to 
the diagram on 
(http://sugino.issp.u-tokyo.ac.jp/esm/index.php?SIESTA%2BESM%20Manual). 
If I do

assume_isolated=esm

esm_bc=bc1

Is the lattice constant for this situation defined as

celldm(1)= L/2 + 4a + L/2

?

Dr. Robert Molt

Indiana University Perdue University

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] How to create Vacuum

[Robert Molt]

Can the input manual's description of esm_bc be discussed further? Can a 
reference be given to exactly how these terms are defined?



On 7/24/17 10:36 AM, Eduardo Menendez wrote:

I think the answer to how to create vacuum is in the example ESM_example.

Let me present a related question. How much can we reduce the width of 
vacuum in the unit cell when using esm_bc='bc1'?


Eduardo Menendez Proupin


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Documentation on Pseudopotentials

[Robert Molt]

Good evening,

I was hoping to be given a reference to understand the differences in 
the QE pseudopotential names; I do not understand how to correlate 
differences in the names with different papers from which they 
originate. For example, on the page


http://www.quantum-espresso.org/pseudo-search-results/?el_id=1_id=8_id=12_k_id

there are 3 listed pseudopotentials relative to the restrictions I gave. 
However, I do not know how to look up the differences between 
H.pbe-kjpaw.UPF 
 
and H.pbe-kjpaw_psl.0.1.UPF 
 
to understand what I am using.


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Use of mixing_beta

[Dr. Robert Molt Jr.]

Good evening,

I have 2 questions about mixing_beta.

1.) The manual states that mixing_beta is a mixing factor for 
self-consistency. Can someone give a reference to how this is defined, 
mathematically?

2.) I have been able to divine from the forums that it is effectively a 
scaling of of the previous SCF cycle's density 
(http://www.mail-archive.com/pw_forum@pwscf.org/msg01302.html) as it 
relates to the current step's calculation. I appreciate that it improves 
SCF convergence.

Broadly, I am confused why this would be useful to speed up SCF 
convergence. I have written my share of SCF codes for molecules with 
basis functions of (gaussians+spherical harmonics), but am new to plane 
waves and PBCs. In molecular calculations, one never scales the previous 
step's density in an iterative solution (or in solving non-linear 
coupled cluster amplitudes). Is this somehow akin to DIIS histories, in 
some way, to be selective in the previous cycle's estimate?

Thank you for your time,

Dr. Robert Molt
Indiana-University Perdue University
ENSCO

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Proper Symmetry Representation

[Dr. Robert Molt Jr.]

ructure from a cif file from 
http://www.crystallography.net/cod/1010954.html

2.) I have specified the lattice constant as celldm(1)=13.454. I assume 
that the default, Bohr radius, is not affected by selecting the 
"Angstrom" flag later on.

3.) nat, according the manual, specifies the number of atoms in the unit 
cell. Does this mean the total number of atoms, i.e., 18+56 for SiO2 if 
I have selected ibrav=2, or does the code expect the primitive cell atom 
number since that's the Espresso default?

Thank you for your time,

Dr. Robert Molt
Indiana-University Perdue University
ENSCO

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Dead Link on Webpage Concerning Parallel Performance

[Robert Molt]

Good evening,

On the FAQ for parallel execution, there is a reference to section 3 of 
the User Guide. This link seems to be dead, as it redirects elsewhere 
(which does not seem to be the User Guide). The top of the page also 
states "Page Not Found."


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum