Dear Tejas,
There are many tests to check and test here. But one thing that comes to
my mind is the pseudopotentials you used. you could try to use another set
of pseudopotentials (especially for N). Try the recommended set here:
https://www.materialscloud.org/discover/sssp/table/efficiency.
Dear Tejas,
Did you test giving an initial magnetic moment to N instead of W?
For example:
starting_magnetization(2)= 0.5
Regards,
Mostafa
AUC
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Dear Samare,
You are performing 'scf' calculation for Ti-doped Fe2O3 under electric
field. This gives only the electron's response to the field. If you are
interested in ions response (and in fact the ion-electron response) , you
may need to use 'relax'. Of course make sure to relax the zero
Dear Rostami,
As I explained in a recent thread, the raw dipole printed out by pw.x is
not meaningful. One needs to post-process the results. Please see here:
https://www.mail-archive.com/users@lists.quantum-espresso.org/msg39910.html
Few other observations:
1- Your k-points mesh does not look
Dear Terry,
The dipole results need post-processing. One needs to subtract n x
polarization quantum to obtain a meaningful polarization. n is an
integer.
Consider a simple dielectric like MgO at zero field. pw.x may give you
different dipoles in all directions, although physically in all
Dear Tejas,
I see two issues:
1) Your supercell size is too small. This corresponds to a high
concentration of N. I would go for 4x4x4 conventional cells of W. That is
128 atoms.
2) A magnetic moment on N is needed since the odd number of electrons is
because of N.
Regards,
Mostafa
AUC
Dear Yasser,
Thank you for your response and suggestion. I agree that DFT+U would
improve the electronic structure of Fe-oxides, but the problem I'm facing
is more related to symmetry. But to confirm this, I did actually try a
quick DFT+U calculation and I still have the same problem that some
in the
conventional cell.
Best Regards,
Mostafa Youssef
AUC - Egypt
# Input file for the primitive cell
calculation = 'vc-relax' ,
verbosity = 'high' ,
restart_mode = 'from_scratch' ,
prefix='fe2o3' ,
outdir='/data/mostafa/Fe2O3/fix_magnet_strucutre2/scratch/' ,
pseudo_dir = '/home/mostafa
Dear Laurens,
When I get this error, it is typically due to a parallelization issue.
A quick fix that worked for me is using -ndiag 1 , so for example:
pw.x_location -ndiag 1 output_file.
Check the manual and forums for more details.
Regards,
Mostafa Youssef
AUC, Egypt
Dear Krishnendu,
If you model the alloy using a unit cell, then you are modeling a very high
Nb concentration ordered alloy.
Take HCP unit cell having two Zr atoms. If you replace one with Nb, then
you get 50%-50% Zr-Nb.
There is no way to avoid forming a supercell of Zr (Say 54 atoms) and then
Dear Lance,
When I get this error, it is typically due to a parallelization issue. A
quick fix would be using -ndiag 1 , so for example:
pw.x_location -ndiag 1 output_file.
Check the manual and forums for more details.
As a side, I highly doubt that these Mn and O pseudopotentials
Dear Jibiao,
If you would like to use modern theory of polarization (MTP) version of
applying the electric field and reach 1 Ry a.u., then you can do this
gradually. So converge 0.1 a.u., keep the wave functions, and use them as
initial guess to 0.2 a.u.. Repeat with steps of 0.1 a.u. until you
Dear Jibiao Li,
A field of 1 Ry a.u. is giant and atypical, so one should not be surprised
do not converge. Recall, 1 in Ry a.u.=36.3609*10^10 V/m.
I also noticed that you impose fixed occupations and then apply Gaussian
smearing. Those are in contradiction of each other. Apparently the code
Dear AT Raji,
A sample input file will help clarifying the issue.
My guess is that you are dealing with a system with complex potential
energy landscape and multiple local minima. If you know that the total
magnetization has to be zero and you are using smearing, then try giving
small
Dear Sayan,
In the case of metallic systems, it is recommended to use smearing. With the
smearing applied, you can use start_magnetization to give an initial guess for
the magnetic moment. pw.x will try self-consistently to find the final
magnetization that leads to minimum energy (Achieving
Dear Sayan,
1- nspin=2 works whether you use LDA or GGA.
2- start_magnetization works when you apply smearing (occupation tag). Using
this tag you give an initial guess and let the code to find the final
magnetization associated with some nearby local energy minimum.
tot_magnetization works
Dear Mohammadreza,
Have a look at this link:
http://materialscloud.org/sssp/
Also here:
http://qe-forge.org/gf/project/pslibrary/
Regards,
Mostafa
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Dear Subhodip,
I'm no expert in high pressure physics and one needs to know the specifics of
the system.
How much pressure are you applying ? If too much the whole pseudopotential
approach cannot be very helpful. Are you able to get reasonable phonons at
zero pressure ? Do you anticipate
Dear Subhodip,
If you maintain the lattice constant resulting from vc-relax then the pressure
effect should be there in your phonon calculations. You apply the pressure by
constraining the volume.
Regards,
Mostafa
MIT
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Dear Zara,
Have a look at :
http://journals.aps.org/prx/abstract/10.1103/PhysRevX.4.031044
Regards,
Mostafa
MIT
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Resolved. Clicking the box "Render +/- isovalue" restores the default red and
blue colors.
Mostafa
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Dear all,
This is an Xcrysden usage question, but since most QE users use Xcrysden, I'm
posting here as well.
I'm using xcrysden version 1.5.60 on windows using cygwin. The default color
for 3D isosurface is yellow. However, in older versions it was red (+) and
blue (-). For consistency
Dear David,
In experiments , neutral O2 gas leaves the TiO2 crystal causing the creation of
oxygen vacancies behind. However, these vacancies can have any charge state.
Neutral in which the two electrons (reminiscent of O2- ion) set around the
vacancy forming polarons, 2+ in which the two
that calculating
the formation energy of Nd defects in TiO2 requires a reference state for Nd;
for example Nd2O3.
Regards,
Mostafa Youssef
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Dear Mohammad,
Yes you can simulate electric field effect on bulk 3D material. In pw.x input
description check lelfield = .true.
Also check these two papers:
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.89.157602
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.89.117602
Dear Evan,
The postprocessing utility pp.x can calculate and plot the average potential as
a function of x or y or z. This can help in performing the potential alignment.
Regards
Mostafa Youssef
MIT
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Dear Nkosinathi,
Please send atomic positions and cell vectors and I can test it.
Regards,
Mostafa
MIT
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I'm not very familiar with ESM model. But certainly modeling Na+ in water (or
any insulator) requires tot_charge=+1. For MD , or relaxation nothing else is
needed.
Regards,
Mostafa
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Also note that you have one sodium atom and you did not set tot_charge to +1.
So you are actually modeling Na+ and an electron. It is very difficult to
predict the outcome of this calculation (metallic solution vs. insulating one)
in a vc-relax calculation. If your goal is to model Na+, then
Dear Nkosinathi,
What is exactly not converging , the electronic minimization, or the ionic?
Few things to note:
1- 90 H2O molecules +ion is 181 nat not 91.
2- It is a bit strange to use mp smearing typical for metals with liquid water.
But it is unlikely that this is the cause of the
Dear Zara,
Please have a look at this tutorial
http://theossrv1.epfl.ch/Main/OxidationStates
Regards,
Mostafa
MIT
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Dear Lei,
If your material is does not exhibit large electrostriction and piezoelectric
effect , then you can ignore changes in lattice parameter. Other wise you need
to generate multiple curves (energy vs. volume) each curve has a different c/a
ration. Where c is the direction parallel to
Dear Ozan,
Make sure that all three files have same supercell vectors and same FFT grid.
Mostafa
MIT
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K_POINTS automatic
1 1 1 1 1 1
This works.
Mostafa
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Dear Parham,
I never studied quantum dots , so I cannot give a particular recommendation.
But for the electric field in Berry phase formalism I can say that Gamma point
only is not implemented in pw.x but it the default and only option in cp.x. In
pw.x you can use one kpoint but it has to be
Dear Sakhraoui,
The format of .XSF is explained here:
http://www.xcrysden.org/doc/XSF.html
You can plot rho_up -rho_down using plot_num=6 option in pp.x
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html#idm6483344
Regards,
Mostafa
MIT
Dear Suresh,
I think the reason is the Ti pseudopotential. This one has 4 valence electrons
and freezes the rest. This leads to larger ionic sizes and overestimation of
the lattice constant. Allowing more Ti valence electrons, means further
relaxation for the outer electronic shell and
Dear Andrey,
I'm not particularly familiar with Al2O3 surfaces, but in general cutting
rectangular surfaces can be accomplished in many cases by cutting the same
surface from primitive cell instead of the conventional well.
For example (111) is not rectangular in tetragonal Hf2O based on the
Dear Subhodip,
Check example04 provided with pw.x. You can find it in:
/Espresso_folder/PW/examples/example04
>From README:
example04:
This example shows how to calculate the polarization via Berry
Phase in PBTiO3 (contributed by the Vanderbilt Group in Rutgers
University).
I
a.s.r.
Is there a way to enforce epsilon calculations based on frequencies after a.s.r
application ?
I'm using Q.E.5.2.0 but I believe recent versions do not have updates in this
part of the code.
Thank you,
Mostafa Youssef
MIT
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Dear Dae Kwang Jun
Equation (1) that you wrote is the correct one.
And you are right bulk V_AlAs and bulk V_GaAs are obtained in a similar way as
in the interface but you need bulk cells. Their values can be anything ,
positive or negative it does not matter and in fact they are arbitrary.
Dear Dae Kwang Jun
In addition for each bulk calculation one needs to calculate the bulk average
electrostatic potential. Then for each compound you refer its EVBM to the
electrostatic potential calculated in its bulk (not yet the interface). Only
then you can use the interface
Dear Dae Kwang Jun,
You also need 2 bulk calculations for AlAs and GaAs to get their band edges
with respect to to their bulk electrostatic potentials. Then you can use the
interface potential to align the band edges of the two semiconductors. It
looks like you missed this step.
Mostafa
Dear Evan,
I would consult literature for that matter. It is very difficult and
counterproductive to discuss this in an online forum.
Mostafa
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Correction:
I-A= E(N+1)+E(N-1)-2E(N)
Mostafa
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Dear Reza,
If hydrogen can transform to Silicon than Quantum Espresso is an all Nucleon
code that simulates Fusion :-)
Check your Pseudo !
Regards,
Mostafa
MIT
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Dear Evan and Layla,
E(N+x) where x is a real number can be calculated using tot_charge:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm6396048
The ionization potential is not well-defined in bulk as Layla described but the
difference I-A is well-defined for bulk.
ased on the lattice parameters and supercells that the authors
reported.
In computing the K-S gap of a neutral cell I would use the tetrahedron method
or fixed occupations (i.e no smearing) and a dense K-point mesh
Regards,
Mostafa Youssef
MIT
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Thank you for clarification, Ryky!
Best Regards,
Mostafa
MIT
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Dear Vipul,
This is an old problem in semiconductor physics. In summary you need 2 set of
calculations. One for a surface (interface) and another one for bulk.
Key papers to review are:
http://journals.aps.org/prb/abstract/10.1103/PhysRevB.35.8154
Dear Varadharajan ,
This paper clarifies a lot of the ambiguities associated with determining the
spontaneous polarization. Particularly the discussion around Fig. 9.
http://arxiv.org/abs/1202.1831
Best,
Mostafa
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Thank you for the clarification, Prof. de Gironcoli. I think I misinterpreted
the meaning of the matrix elements.
Best Regards,
Mostafa
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file.
Thank you,
Mostafa Youssef
MIT
The matrices are:
atom1 Tr[ns(na)] = 2.70769
eigenvalues:
0.142 0.177 0.182 0.417 0.436
eigenvectors:
0.675 0.000 0.000 0.325 0.000
0.000 0.000 0.500 0.000 0.500
0.000 0.000 0.500 0.000 0.500
0.000 1.000 0.000
Dear David,
In principle, starting from a 2D material and applying vc_relax should end up
with the 3D version of the material. That is in the graphene case you should
end up with graphite upon complete convergence. I doubt that this simulation
is your intention here.
If you would like ,
.
Best Regards,
Mostafa
MIT
From: Mehmet Topsakal [mtops...@umn.edu]
Sent: Thursday, March 10, 2016 3:58 PM
To: PWSCF Forum; Mostafa Youssef
Subject: Re: [Pw_forum] Ultrasoft or Norm conserinvg PP for Ce
Dear Mostafa,
Please find our PAW potentials for rare-earth
Dear all,
I wonder if there is a reasonably performing Ce PP, US or NC , with 12 valence
electrons and non-linear core correction.
Thank you,
Mostafa
MIT
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Dear Giuseppe,
The ethylene rotation example you mentioned is very interesting. I wonder if
there is a reference you recommend that carefully analyzed this case with DFT
or other quantum chemical approaches.
Best Regards,
Mostafa
MIT
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bservation was discussed in this
article: http://www.nature.com/nature/journal/v453/n7196/full/nature07009.html
(It is also fun and instructive to follow the debate that this paper raised in
literature!)
Best Regards,
Mostafa Youssef
MIT
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can help in clarifying this.
Mostafa Youssef
MIT
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Dear Victor,
I think there is nothing fundamentally wrong with calculating DOS from
snapshots obtained from finite T MD. I also have seen this once in the
literature from the work of Prof. A. Selloni group on TiO2/water interfaces
somewhere around 2010.
One could argue that even the single
Dear Stephan,
The ONCV are norm conserving so 4*ecutwfc should be fine.
Mostafa Youssef
MIT
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Dear Phil and all,
Note that for a functional with exact exchange, the difference between
ionization potential and electron affinity (I-A) is not the same as the
Kohn-Sham single particle states gap. The consensus, as far as I know, is
that I-A is more physical and relevant to comparison
Dear Manhong,
As far I know the incosistency of treating charged defects within PAW formalism
discussed in PHYSICAL REVIEW B 89, 045116 (2014) has not been resolved in any
pseudopotential code. I wish I can devote more time to study this paper more
carefully.
Regarding the second paper,
Dear Yusuf,
I'm not a developer but from my limited experience, I can tell that
cell_dofree tag (the key to apply uniaxial strain) works well with DFT+U (With
NC and USPP, I'm not sure about PAW). Finite electric field with DFT+U (NC and
USPP) seems to work well too based on few tests I
This question is resolved. I understand a little better now that in small
field regime one solves for polarized Bloch states and as such the charge
density is indeed periodic.
Mostafa
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the non-periodicity of the scalar potential is avoided.
Any thoughts or references are highly appreciated.
Mostafa Youssef
MIT
MgO_poential.pdf
Description: MgO_poential.pdf
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Dear Reza,
Exploring the potential energy surface of glassy systems is not a trivial
problem not to mention impurities in glassy systems. Depending on how deep you
want to explore this, you may want to explore PLUMED package which is
compatible with PWscf.
http://www.plumed-code.org/
For
Dear Reza,
In addition to what Lorenzo suggested in relation to the accuracy of DFT in
describing the band gap, there is a possibility that point defects can play a
role in reducing the gap as the temperature increases. You might need to
inspect the literature more to see how the observed
The last time report I quoted is with Hubbard U and this in fact what I
typically find in PWscf relaxation calculation.
I will send you the two output files offline. Thank you very much for your help!
Regards,
Mostafa
MIT
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Thank you for replying, Prof. Giannozzi. I'm using version 5.2.0, the system
has 135 atoms of which 108 has U correction. I'm running it on 32 processors
with 1 pool, a serial algorithm for Linear algebra to avoid "error in Cholesky
decomposition", and 1 task group.
I'm a bit surprised
and is there a
recommended possibility to reduce force calculation time?
I attempted using Norm Conserving PP's but unfortunately I could not get the
code pass the 1 ionic step because of the S matrix not being positive definite.
I appreciate your thoughts on this.
Regards,
Mostafa Youssef
MIT
Dear Fei
As the message indicates there is a problem in reading the norm conserving
pseudopotential file. I think this may also be the reason why example01 did not
work because it uses NC PP for Si.
Try the attached version of the H and O PP used in the H2O test. The attached
worked for me.
Hi Elham,
Testing Pseudopotentials and choosing optimal ones is a daunting task that
needs some serious work. In addition to the valuable advice you quoted from
Prof. de Gironcoli, I'd add that converging total energy will lead you to a
very safe e_cut and rho_cut but probably one can afford a
Hi Fei Mao,
Please post the error message in the file b3lyp-h2o.out. Apparently the test
stopped when it encountered error message here.
M. Y.
MIT
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Hi Sridhar,
Of course you can do this mix. Please have a look at:
http://www.quantum-espresso.org/faq/pseudopotentials/#2.3
M. Y.
MIT
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calculations. The first at zero
field but still with lelfield=.true., the second starts from the wave functions
generated from the first but has the magnitude of the field you would like to
apply. Please see example 10 in PW/examples.
Mostafa Youssef
MIT
Thank you very much for fixing this, Prof. Giannozzi !
Best Regards,
Mostafa Youssef
MIT
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Thank you, Prof. Giannozzi. I tested one more time and found out that by
removing tqr=.true. it works on 8 processors even with an FFT grid of 36x36x36.
With tqr=.true. , the FFT grid has to be multiples of 8.
Best Regards,
Mostafa Youssef
MIT
be overlapping or
increase ecutrho
And the code stops at the first scf step. When I double the energy and charge
density cutoffs , it works well in parallel. This behavior is reproduced in
versions 5.1.1, 5.1.2, and 5.2.0.
Any thoughts on the possible reasons are appreciated.
Thank you,
Mostafa
of U on TiO2 phonons.
Mostafa Youssef
MIT
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a systematic investigation of the performance of
DFT+U in predicting vibrational free energy *differences* between a perfect
crystal (TiO2) and a defective one (TiO2-x) for this class of materials. I
would be very interested if somebody can point out to a paper that addressed
this.
Mostafa
approximation with Parlinski et
al interpolation. Please follow the instructions on PHONOPY website.
Mostafa YOussef
MIT
P.S. Somehow I read the title of your thread as DFT+U cartoons !
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is possible (of
course starting from some initial guess).
Mostafa Youssef
MIT
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that the authors of this paper implemented Wannier on the fly which I
think is not available in Q.E. But the computational cost to re-track the
trajectory and calculate MLWF should not be too expensive if one already
affords the MD run.
Mostafa Youssef
MIT
Dear Bahadir
First, charged slabs are problematic because their total energy does not
converge with respect to vacuum thickness. You can test on a simple model.
However, there is a trick to go around this by inserting a dopant far a way
from the critical reaction zone. For example suppose
>if you can please give me more details about how to control the number of cell
>relaxed , because it is the same with
>different press-conv-thr . for example I want to relax only the c axis keeping
>a and b fixes, by using cell-dofree='z' ,
>but I would give the number of c which i want to
Hi Shaofeng,
Relaxation will give you "a" structure but most likely it is not a
representative structure. MD will give you a set of possibly meaningful and
representative solvation structures. If you average over these meaningful
structures, you can get useful information about the
Hi Imène,
I guess the sopping criterion is press_conv_thr.
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idp365664
Mostafa Youssef
MIT
<http://www.mail-archive.com/search?l=pw_forum@pwscf.org=from:%22Im%C3%A8ne+Ch%C3%A9ra%C3%AFr
!
Mostafa Youssef
MIT
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-content/uploads/Doc/INPUT_PW.html#idp110032
Mostafa Youssef
MIT
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Hi Galvin,
Examining the energies and stresses you obtain from your calculations by the
eye is not a very accurate way to obtain the lattice parameter that minimizes
the energy and corresponds to a zero pressure. More accurate is to fit your
results to an equation of state such as
Thank you very much for addressing my questions, Prof. Giannozzi ! I will keep
the mailing list updated if I succeed in reasonably getting smearing work with
finite electric fields.
Mostafa Youssef
MIT
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under pressure. (Of course with the implicit
warning that the enthalpy inherits the uncertainty in the polarization quantum).
Thank you,
Mostafa Youssef
MIT
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uot; value of the spontaneous polarization of the
material.
A favorite of mine which go over some of these difficulties is this paper:
http://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.014113
Mostafa Youssef
MIT
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Hi Carlo
Both pslib0.31 (http://theossrv1.epfl.ch/Main/Pseudopotentials) and pslib1.0.0
(http://qe-forge.org/gf/project/pslibrary/) have relativistic PP for those two
elements.
Mostafa Youssef
MIT
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http
Thank you very much for your reply, Prof. Dal Corso. And of course many thanks
for the development of the library!
Mostafa Youssef
MIT
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depending on the functional.
Thank you in advance for reading and help!
Mostafa Youssef
MIT
Fe_16e_pslib0.3.pdf
Description: Fe_16e_pslib0.3.pdf
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Hi Mojtaba,
Providing an input file could help in resolving the problem you have. Also
performing few convergence tests on the cutoff for energy and charge density
could help in getting fruitful results with the pseudopotential.
Mostafa Youssef
MIT
for example:
http://journals.aps.org/prb/abstract/10.1103/PhysRevB.90.115120
Mostafa Youssef
MIT
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here
http://www.qe-forge.org/gf/project/pslibrary/frs/?action=FrsReleaseBrowse_package_id=41
Mostafa Youssef
MIT
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