from:"Fabiana Da Pieve"

[Wien] exciton trapping

2012-03-01 Thread Fabiana Da Pieve

Hello wien2k users

I am maybe going to ask a trivial or a totally non-sense question, but I am
trying to do what I can with what I have.
I know that at the moment BSE calculations with wien2k (and other codes)
are very computationally demanding, and in any case the BSE part is still
not released.

In any case, even if it would be released, I think I could not run it on my
system because it is very heavy.
However, I would like to find a way (even a very simple one) to see if a
certain optical excitation would lead to a localized exciton (which
localizes because of local distortion for example) or if such optical
excitation would not lead to any distortion. I would like to study this
because sometimes excitonic transitions could change bond lengths and
change (slightly, I think) the covalency of a certain bond, and in such
distortion the exciton could be trapped, which is want I want to see.

So, I was thinking that MAYBE I could have "a first idea" of the eventual
distortion induce by my optical ideal exciton already at the DFT level in
the following way:

1) I remove an electron from one of the external levels of the anion in
which I believe the hole is created in the file..(ok, very bad thing,
optical excitations cannot be described as localized on a single site at
the beginning)
2) at this point, either I smear the charge uniformly in space  (or maybe I
could explicitly put an electron more in the orbital of the cation which I
know is the acceptor orbital ??)
3) instead of running a normal scf calculation, I run a structural
optimization calculation (keeping the lattice parameters fixed, i.e. moving
only atoms)
4) at the end I analyze the changes in the bond lengths near the atom

Is it correct (at least as a very zero approximation to the problem) ?
totally wrong ?
Any suggestions is welcome !

Thanks !
Fabiana
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[Wien] exciton trapping

2012-03-01 Thread Fabiana Da Pieve

Hello

thanks for the suggestion ! I wanted to try to avoid it because my
sistem is superheavy and...already normal ground state calculations
are quite demanding, but yes, you are right.

Thanks

2012/3/1, Laurence Marks :
> At least with Wien2k you cannot tell the electrons where to go.
>
> Have you looked at the optic code results?
>
> ---
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu 1-847-491-3996
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought"
> Albert Szent-Gyorgi
>  On Mar 1, 2012 2:47 AM, "Fabiana Da Pieve" 
> wrote:
>
>> Hello wien2k users
>>
>> I am maybe going to ask a trivial or a totally non-sense question, but I
>> am trying to do what I can with what I have.
>> I know that at the moment BSE calculations with wien2k (and other codes)
>> are very computationally demanding, and in any case the BSE part is still
>> not released.
>>
>> In any case, even if it would be released, I think I could not run it on
>> my system because it is very heavy.
>> However, I would like to find a way (even a very simple one) to see if a
>> certain optical excitation would lead to a localized exciton (which
>> localizes because of local distortion for example) or if such optical
>> excitation would not lead to any distortion. I would like to study this
>> because sometimes excitonic transitions could change bond lengths and
>> change (slightly, I think) the covalency of a certain bond, and in such
>> distortion the exciton could be trapped, which is want I want to see.
>>
>> So, I was thinking that MAYBE I could have "a first idea" of the eventual
>> distortion induce by my optical ideal exciton already at the DFT level in
>> the following way:
>>
>> 1) I remove an electron from one of the external levels of the anion in
>> which I believe the hole is created in the file..(ok, very bad thing,
>> optical excitations cannot be described as localized on a single site at
>> the beginning)
>> 2) at this point, either I smear the charge uniformly in space  (or maybe
>> I could explicitly put an electron more in the orbital of the cation which
>> I know is the acceptor orbital ??)
>> 3) instead of running a normal scf calculation, I run a structural
>> optimization calculation (keeping the lattice parameters fixed, i.e.
>> moving
>> only atoms)
>> 4) at the end I analyze the changes in the bond lengths near the atom
>>
>> Is it correct (at least as a very zero approximation to the problem) ?
>> totally wrong ?
>> Any suggestions is welcome !
>>
>> Thanks !
>> Fabiana
>>
>>
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>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>>
>

[Wien] about some output files from wien2k

2013-06-20 Thread Fabiana Da Pieve

Dear Wien2k community

I am trying to interface some output files from wien2k (.vcoul, .r2v,
clmsum and .corewavefunction) with a home-made code (this code is much
much simpler and trivial with respect to the big purposes of wien2k) .

- is it possible to split out these files directly when running run_lapw ?
(without passing through lapw5, or xspec, or telnes)

- are you aware if there is any way to obtain such files (in the same
format as they are printed by wien2k), by one of the others FLAPW
codes somehow interfaced with wien2k, working either in
TDDFT-bootstrap (elk) or G0W0 (exciting) ?
I have checked some web sites and I did not find any precise comments
about "same output of wien2k" or things like that. Maybe my thought
that all these tools had somehow similar output files was wrong.

Thank you very much in advance
Fabiana

VUB, Brussels
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Re: [Wien] about some output files from wien2k

2013-06-20 Thread Fabiana Da Pieve

Dear Prof. Blaha

thank you very much for your answer, but...

1) for the printing of specific corewavefunction maybe you meant to
activate the printing option in .inc, and not .inm , right ?
I do NOT see the way to switch on such printing option in .inm

2) About other flapw codes, ok, I thought that the other two codes
were somehow born as "branch" of wien2k...and so I have the hope of
some similarity with the output of wien2k.
Then, forgetting about TDDFT-bootstrap or G0W0, is there any
application of mBJ on organic molecular crystals ?

I have checked a bit over google, and did not find anything
(neglecting vdW corrections would be ok for me)

Thank you very much in advance
Fabiana




2013/6/20, Peter Blaha :
>> I am trying to interface some output files from wien2k (.vcoul, .r2v,
>> clmsum and .corewavefunction) with a home-made code (this code is much
>> much simpler and trivial with respect to the big purposes of wien2k) .
>>
>> - is it possible to split out these files directly when running run_lapw
>> ?
>> (without passing through lapw5, or xspec, or telnes)
>
> The files you were mentioning can all be obtained also during scf. (Most
> of them are actually NOT produced by lapw5,xspect,...)
> It requires to set   "R2V" in case.in0 or activate the core-wf printing
> in case.inm. These switches are "off" by default, but can be activated
> anytime.
> clmsum is anyway the main output of an scf calculation.
>
> PS: I doubt that other FLAPW codes have the same output format.
>
>> - are you aware if there is any way to obtain such files (in the same
>> format as they are printed by wien2k), by one of the others FLAPW
>> codes somehow interfaced with wien2k, working either in
>> TDDFT-bootstrap (elk) or G0W0 (exciting) ?
>> I have checked some web sites and I did not find any precise comments
>> about "same output of wien2k" or things like that. Maybe my thought
>> that all these tools had somehow similar output files was wrong.
>>
>> Thank you very much in advance
>> Fabiana
>>
>> VUB, Brussels
>> ___
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>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>
> --
>
>P.Blaha
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWWW:
> http://info.tuwien.ac.at/theochem/
> --
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[Wien] issues related to mBJ

2013-07-22 Thread Fabiana Da Pieve

Dear Wien2k community

I have 3 simple questions about mBJ and one issue (again related to mBJ) on
some files that I would need to plug into my code, once they are printed at
the end of the mBJ calculation. These files are: .vcoul, .r2v, and .clmsum

1) I have nicely done the GGA SCF calculations for my compounds. The
calculation has printed the three files cited above.

2) now, for wien2k_11.1, the steps to do an mBJ calculatiion were:

a) cp $WIENROOT/SRC templates/case.inm vresp case.inm vresp
b) run one more scf-cycle (use run lapw -NI -i 1) to generate the required
case.vresp*
files.
c) “save” the LDA (PBE) calculation
d) edit case.in0 and change the functional to option indxc=28.
e) cp case.in0 case.in0 grr and change indxc in case.in0 grr to 50
f) edit case.inm and change to PRATT mixing.
g) run another scf cycle.

First: my step b) is lasting for a bit too much time. I mean, it is only
one scf cycle...but, I do not know why, it is lasting really too long.
Maybe it is necessary to change the value of the mixing parameter in .vresp
to a lower value (0.2 for example) already at step a), when one copies such
file from SRC_template ?

Second: I guess step g) is NOT simply another single SCF cycle (-i 1), but
more than one. Am I wrong ?

Third: when one is arrived at completing step g, I guess that the files
.vcoul, .r2v and clmsum are printed again, now in the mBJ picture. Right ?

Fourth: if the question to the third answer is yes, then I would like to
know if such files (especially vcoul and r2v) contain ALL the necessary
information related to the potential.

I try to explain myself better. I would like to recycle a real space code
(let's call it code B) which can indeed read some files from wien2k (code
A), and that can do calculations either with multiple scattering in the
muffin tin approximation or with full potential mode (this option is based
on the finite difference method). I have already interfaced this full
potential MS code to another code that calculates resonant excitations
(code C). However, now, I am asking myself if I can really give the vcoul,
r2v and clmsum file to such codes (B and C)  when calculation from A is
mBJ or any other hybrids. I cannot ask to the one who developed long time
ago the code B, and in any case it seem only LDA was used at that time to
be plugged in into such code.  Now, I guess that the files .vcoul and .r2v
(and clmsum) are related to the region INSIDE the spheres, so if I plug
these files into my codes (B and C) I somehow I loose the non-local
contribution outside the spheres, if my calculation with wien2k was done
with mBJ or an hybrid functional.  Am I saying something completely wrong ?
Am I missing something ?

Thank you very much for your attention
Fabiana

VUB, University of Brussels
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Re: [Wien] issues related to mBJ

2013-07-23 Thread Fabiana Da Pieve

Dear Prof. Blaha

thank you very much for your answer about my Tran-Blaha-mBJ issues.

It seems that the code (the one I would use as intermediate step between
wien2k and my code for resonant excitations) reads both expansion in the
sphere and between the sphere. Then the potential is calculated everywhere.
If the mufin tin radius is bigger than in Wien2k, then the code calculates
the corresponding part from the expansion in plane wave of Wien2k.

I am still digging into the different routines but for the moment it seems
that what is done is correct.

Thank you very much for your answer

Fabiana

VUB, Free University of Brussels




2013/7/23 Peter Blaha 

> 1) I have nicely done the GGA SCF calculations for my compounds. The
>> calculation has printed the three files cited above.
>>
>> 2) now, for wien2k_11.1, the steps to do an mBJ calculatiion were:
>>
>> a) cp $WIENROOT/SRC templates/case.inm vresp case.inm vresp
>> b) run one more scf-cycle (use run lapw -NI -i 1) to generate the
>> required case.vresp*
>> files.
>> c) “save” the LDA (PBE) calculation
>> d) edit case.in0 and change the functional to option indxc=28.
>> e) cp case.in0 case.in0 grr and change indxc in case.in0 grr to 50
>> f) edit case.inm and change to PRATT mixing.
>> g) run another scf cycle.
>>
>> First: my step b) is lasting for a bit too much time. I mean, it is only
>> one scf cycle...but, I do not know why, it is lasting really too long.
>> Maybe it is necessary to
>> change the value of the mixing parameter in .vresp to a lower value (0.2
>> for example) already at step a), when one copies such file from
>> SRC_template ?
>>
>
> This is just one iteration of an scf cycle, which is necessary to provide
> case.vresp needed
> for the mBJ potential. It should take (nearly) exactly the same time as a
> single scf-cycle
> of a GGA calculation.
>
>
>> Second: I guess step g) is NOT simply another single SCF cycle (-i 1),
>> but more than one. Am I wrong ?
>>
>
> Yes, this should of course be a full scf-calculation (usually with MANY
> cycles, since in particular
> in your old wien2k-version it may have difficulties with convergence.
>
>
>  Third: when one is arrived at completing step g, I guess that the files
>> .vcoul, .r2v and clmsum are printed again, now in the mBJ picture. Right ?
>>
>
> Since mBJ requires R2V in case.in0, you get at the end the scf-mBJ vcoul,
> r2v and clmsum files.
>
>
>  Fourth: if the question to the third answer is yes, then I would like to
>> know if such files (especially vcoul and r2v) contain ALL the necessary
>> information related to the
>> potential.
>>
>
> Yes, vcould and r2v contains ALL the information. At the beginning the
> radial coefficients of the
> angular momentum expansion are printed, at the end the fourier
> coefficients of the potentials.
>
>
>  I try to explain myself better. I would like to recycle a real space code
>> (let's call it code B) which can indeed read some files from wien2k (code
>> A), and that can do
>> calculations either with multiple scattering in the muffin tin
>> approximation or with full potential mode (this option is based on the
>> finite difference method). I have
>> already interfaced this full potential MS code to another code that
>> calculates resonant excitations (code C). However, now, I am asking myself
>> if I can really give the
>> vcoul, r2v and clmsum file to such codes (B and C)  when calculation from
>> A is  mBJ or any other hybrids. I cannot ask to the one who developed long
>> time ago the code B,
>> and in any case it seem only LDA was used at that time to be plugged in
>> into such code.  Now, I guess that the files .vcoul and .r2v (and clmsum)
>> are related to the region
>> INSIDE the spheres, so if I plug these files into my codes (B and C) I
>> somehow I loose the non-local contribution outside the spheres, if my
>> calculation with wien2k was
>> done with mBJ or an hybrid functional.  Am I saying something completely
>> wrong ? Am I missing something ?
>>
>
> As mentioned above, these files contain the potential for the spheres
> (both, the spherical (muffin-tin) and
> non-spherical contributions. But these files contain also the info about
> the interstitial.
>
> If your codes A,B or C are multiple scattering codes which have ONLY
> "spheres" (overlapping ones ?),
> you need to expand the interstitial potential into spherical harmonics
> ("increasing our atomic spheres
> to yours"). This was discussed  some time ago (1-2 years) in several
> emails on the mailing list.
>
> PS: Everything said above holds for "local" potentials (like mBJ). A
> "hybrid" DFT cannot be represented
> that way and these potentials files contain only then only the local part,
> but not the non-local HF.
>
> --
> --**---
> Peter Blaha
> Inst. Materials Chemistry, TU Vienna
> Getreidemarkt 9, A-1060 Vienna, Austria
> Tel: +43-1-5880115671
> Fax: +43-1-5880115698
> email: pbl...@theochem.tuwien.ac.at
> ---

Re: [Wien] init mbj lapw command not found

2013-07-24 Thread Fabiana Da Pieve

Dear Yundi Quan

you should look at the usersguide related to the version that you are
using.
For version 11 indeed, the command init_mbj_lapw does not exist and the way
to prepare a mBJ calculation is a bit different. .
You can find a pdf of the userguide of your version in the directory
wien2k-11/SRC_usersguide_html

Just look for the paragraph about mBJ.

Regards
Fabiana






2013/7/23 Yundi Quan 

> Hi,
> I use WIEN2k_11. I want to do mBJ calculations. But command
> init_mbj_lapw could not be found. Where is it?
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[Wien] about "c" in TB-mBJ for open structures

2013-08-15 Thread Fabiana Da Pieve

Dear wien2k developers and users

I am checking the performance of Tran-Blaha mBJ with respect to GW
(non self consistent, for the moment) for some organic crystals (quite
open structures). For some of them the improvement with respect to LDA
(my starting point for G0W0) is good, for some others it is still
pretty good but I would like to have a better result. Prof. Blaha
suggested sometime ago to use the "c" parameter from bulk graphite,
since the scf calculation  of the "c" parameter of TB-mBJ in suh open
structures could have not so much sense.

I am using Wien2k_11.1. Could you please confirm that the procedure I
am going to use (reported here below) is correct ?
(I just want a confirmation of what I read in the manual for this
version at page 50,
or IF THERE IS SOMETHING MORE THAT I SHOULD DO and that I did not
catch from the manual).

I will do a bulk calculation for graphite, then take the graphite.grr
file, copy it into the orgcrystal.grr ; then I will cancel  the
orgcrystal.in0_grr file and then I will run finally the mBJ self
consistent run. The value inside the .grr file (which will be indeed
the one corresponding to bulk graphite) will be read by the scf mBJ
run.

(sorry to ask, but my contract finishes soon and I cannot allow myself
to do stupid errors...)

Thank you very much
Fabiana

VUB, Free University of Brussels
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Re: [Wien] about "c" in TB-mBJ for open structures

2013-08-15 Thread Fabiana Da Pieve

Thank you very much Dr. Tran for your answer.

Well, maybe the suggestion by Prof. Blaha about using the "c" from a
calculation on graphite was because graphite has, at least, the C
atoms, which are the backbones bonds in organic crystals, and it has a
layered structure, as organic crystals, but organic crystals are muh
more "open" structures.

Anyway, I will maybe give it a trial anyway, and report to the mailing
list. Maybe indeed nothing will really change in terms of the band
gap.

Thanks
Fabiana

2013/8/15, t...@theochem.tuwien.ac.at :
> Hi,
>
> The mBJ potential can certainly not be used for systems with infinite
> vacuum (e.g., isolated molecule, surface), but for open structures the
> results can (maybe) still be ok without fixing "c" to some value
> (I have not tried myself, but maybe there is already results in the
> literature on open structures). If the gaps that you obtained without
> fixing "c" are not completely wrong, then I do not see any reason
> to fix "c" from a previous calculation.
>
> Also, there is no reason to fix "c" to the one obtained with graphite
> and not another solid. The procedure you mentioned looks ok.
>
> F. Tran
>
> On Thu, 15 Aug 2013, Fabiana Da Pieve wrote:
>
>> Dear wien2k developers and users
>>
>> I am checking the performance of Tran-Blaha mBJ with respect to GW
>> (non self consistent, for the moment) for some organic crystals (quite
>> open structures). For some of them the improvement with respect to LDA
>> (my starting point for G0W0) is good, for some others it is still
>> pretty good but I would like to have a better result. Prof. Blaha
>> suggested sometime ago to use the "c" parameter from bulk graphite,
>> since the scf calculation  of the "c" parameter of TB-mBJ in suh open
>> structures could have not so much sense.
>>
>> I am using Wien2k_11.1. Could you please confirm that the procedure I
>> am going to use (reported here below) is correct ?
>> (I just want a confirmation of what I read in the manual for this
>> version at page 50,
>> or IF THERE IS SOMETHING MORE THAT I SHOULD DO and that I did not
>> catch from the manual).
>>
>> I will do a bulk calculation for graphite, then take the graphite.grr
>> file, copy it into the orgcrystal.grr ; then I will cancel  the
>> orgcrystal.in0_grr file and then I will run finally the mBJ self
>> consistent run. The value inside the .grr file (which will be indeed
>> the one corresponding to bulk graphite) will be read by the scf mBJ
>> run.
>>
>> (sorry to ask, but my contract finishes soon and I cannot allow myself
>> to do stupid errors...)
>>
>> Thank you very much
>> Fabiana
>>
>> VUB, Free University of Brussels
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[Wien] the "c" parameter in TB-mBJ

2013-08-22 Thread Fabiana Da Pieve

Dear Wien2k developers and users

I am running several TB-mBJ calculations to be compared with some GW
results for organic crystals. My aim is to plug the mBJ .vcould and .r2v
into a code for resonant spectroscopies (if it comes out that mBJ describes
well the electronic structure of the systems).
The calculations are running and I see that indeed the GGA starting gap is
*slowly* opening, very good sign. But I also would like to check what Prof.
Blaha suggested some time ago, i.e. to use the "c" parameter from
graphite,  as the average of gradrho/rho might be ill-defined for my open
structures.

Now, for my open structures, I needed to choose a certain radius for the
carbon atoms, which is different from the one that wien2k was suggesting
when I constructed the .struct file from an .xsf file.

So, when I launch the calculation for graphite (in order ot use the
resulting "c" parameter also for my open structures), do I have to set the
same radius I have chosen for the carbon atoms for my open structures, or
leave it as it is chosen by Wien2k ?

I think that in the APW method results should be in principle independent
on the choice of the radius (I hope I am not totally wrong here), but I
guess somehow it could influence gradrho/rho.

Thank you very much

Fabiana
VUB, Free University of Brussels
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Re: [Wien] the "c" parameter in TB-mBJ

2013-08-22 Thread Fabiana Da Pieve

Ok, thank you very much for your anwer

But, just to remind you:
> the more the size of the basis set is large, the less the results will
> depend on the choice of the atomic radii RMT.
>
> yes, sure. (I am using a quite big size of the basis set, but if I
increase it more my code for resonant spectroscopies will essentially
explodes !)

Thank you very much

Fabiana










> F. Tran
>
>
> On Thu, 22 Aug 2013, Fabiana Da Pieve wrote:
>
>  Dear Wien2k developers and users
>>
>> I am running several TB-mBJ calculations to be compared with some GW
>> results for organic crystals. My aim is to plug the mBJ .vcould and .r2v
>> into a code for
>> resonant spectroscopies (if it comes out that mBJ describes well the
>> electronic structure of the systems).
>> The calculations are running and I see that indeed the GGA starting gap
>> is *slowly* opening, very good sign. But I also would like to check what
>> Prof. Blaha
>> suggested some time ago, i.e. to use the "c" parameter from graphite,  as
>> the average of gradrho/rho might be ill-defined for my open structures.
>>
>> Now, for my open structures, I needed to choose a certain radius for the
>> carbon atoms, which is different from the one that wien2k was suggesting
>> when I constructed
>> the .struct file from an .xsf file.
>>
>> So, when I launch the calculation for graphite (in order ot use the
>> resulting "c" parameter also for my open structures), do I have to set the
>> same radius I have
>> chosen for the carbon atoms for my open structures, or leave it as it is
>> chosen by Wien2k ?
>>
>> I think that in the APW method results should be in principle independent
>> on the choice of the radius (I hope I am not totally wrong here), but I
>> guess somehow it
>> could influence gradrho/rho.
>>
>> Thank you very much
>>
>> Fabiana
>> VUB, Free University of Brussels
>>
>>
>>
>>
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Re: [Wien] the "c" parameter in TB-mBJ

2013-08-22 Thread Fabiana Da Pieve

Ok, great.

I think I can proceed the way I am doing. (I just needed some confirmations...)
Thank you very much Prof. Blaha for your answer !

Fabiana




2013/8/22, Peter Blaha :
> I do not have experience with mBJ for organic molecules/crystals.
>
> For sure, when simulating an isolated molecule in a big box, the resulting
> grad rho/rho average is "meaningless". For a "real" crystal (even when it
> is
> very loosely packed, it might be ok (or not ?? as mentioned - no own
> experience).
>
> No, different RMT should not produce different grad rho/rho (at least when
> you are
> always fully converged).
>
> Am 22.08.2013 17:33, schrieb Fabiana Da Pieve:
>> Dear Wien2k developers and users
>>
>> I am running several TB-mBJ calculations to be compared with some GW
>> results for organic crystals. My aim is to plug the mBJ .vcould and .r2v
>> into a code for resonant
>> spectroscopies (if it comes out that mBJ describes well the electronic
>> structure of the systems).
>> The calculations are running and I see that indeed the GGA starting gap is
>> *slowly* opening, very good sign. But I also would like to check what
>> Prof. Blaha suggested some
>> time ago, i.e. to use the "c" parameter from graphite,  as the average of
>> gradrho/rho might be ill-defined for my open structures.
>>
>> Now, for my open structures, I needed to choose a certain radius for the
>> carbon atoms, which is different from the one that wien2k was suggesting
>> when I constructed the
>> .struct file from an .xsf file.
>>
>> So, when I launch the calculation for graphite (in order ot use the
>> resulting "c" parameter also for my open structures), do I have to set the
>> same radius I have chosen for
>> the carbon atoms for my open structures, or leave it as it is chosen by
>> Wien2k ?
>>
>> I think that in the APW method results should be in principle independent
>> on the choice of the radius (I hope I am not totally wrong here), but I
>> guess somehow it could
>> influence gradrho/rho.
>>
>> Thank you very much
>>
>> Fabiana
>> VUB, Free University of Brussels
>>
>>
>>
>>
>> ___
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>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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>
> --
> -
> Peter Blaha
> Inst. Materials Chemistry, TU Vienna
> Getreidemarkt 9, A-1060 Vienna, Austria
> Tel: +43-1-5880115671
> Fax: +43-1-5880115698
> email: pbl...@theochem.tuwien.ac.at
> -
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[Wien] an error from lapw1 I cannot get rid of (whatever I do !)

2013-09-13 Thread Fabiana Da Pieve

Dear Wien2k developers and users

now you will kill me because on this question there are already many
things in the mailing list.
I have tried everything possible for this compound (structure file
below) and I yet I did not succeed to make the scf run properly.

I get the error:
Error in LAPW1
 'SELECT' - no energy limits found for L= 0
 'SELECT' - E-bottom -200.0   E-top   -5.68200

I have tried to: reduce Rmt, change the number of k points, change the
mixing factor, change the energy parameters everything that was
suggested in the mailing list and other things that I found on the
userguide. But there is no way ! I failed.

The strange thing is that I am running many other similar compounds,
and I never had any problems (really, they are very similar
compounds).

All suggestions are very much appreciated

Thank you very much for your attention
Fabiana



Wien97 struct file generated by XCrySDen program
P   20
 NREL
 14.886988 13.751427 23.899435 90.01 90.01 90.01
ATOM  -1: X=0.46745645 Y=0.13407779 Z=0.72177357
  MULT= 4  ISPLIT= 8
  -1: X=0.96745645 Y=0.36592221 Z=0.27822643
  -1: X=0.53254355 Y=0.63407779 Z=0.77822643
  -1: X=0.03254355 Y=0.86592221 Z=0.22177357
O  NPT=  781  R0=.00010 RMT=   1.2   Z:   8.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -2: X=0.82401610 Y=0.34963726 Z=0.99052607
  MULT= 4  ISPLIT= 8
  -2: X=0.32401610 Y=0.15036274 Z=0.00947393
  -2: X=0.17598390 Y=0.84963726 Z=0.50947393
  -2: X=0.67598390 Y=0.65036274 Z=0.49052607
O  NPT=  781  R0=.00010 RMT=   1.2   Z:   8.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -3: X=0.65523123 Y=0.98268849 Z=0.83813124
  MULT= 4  ISPLIT= 8
  -3: X=0.15523123 Y=0.51731151 Z=0.16186876
  -3: X=0.34476877 Y=0.48268849 Z=0.66186876
  -3: X=0.84476877 Y=0.01731151 Z=0.33813124
N  NPT=  781  R0=.00010 RMT=   1.2   Z:   7.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -4: X=0.63997780 Y=0.28559270 Z=0.84768142
  MULT= 4  ISPLIT= 8
  -4: X=0.13997780 Y=0.21440730 Z=0.15231858
  -4: X=0.36002220 Y=0.78559270 Z=0.65231858
  -4: X=0.86002220 Y=0.71440730 Z=0.34768142
N  NPT=  781  R0=.00010 RMT=   1.2   Z:   7.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -5: X=0.57914808 Y=0.13124269 Z=0.79711804
  MULT= 4  ISPLIT= 8
  -5: X=0.07914808 Y=0.36875731 Z=0.20288196
  -5: X=0.42085192 Y=0.63124269 Z=0.70288196
  -5: X=0.92085192 Y=0.86875731 Z=0.29711804
C  NPT=  781  R0=.00010 RMT=   1.0   Z:   6.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -6: X=0.75040671 Y=0.23930188 Z=0.92730470
  MULT= 4  ISPLIT= 8
  -6: X=0.25040671 Y=0.26069812 Z=0.07269530
  -6: X=0.24959329 Y=0.73930188 Z=0.57269530
  -6: X=0.74959329 Y=0.76069812 Z=0.42730470
C  NPT=  781  R0=.00010 RMT=   1.0   Z:   6.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -7: X=0.77021191 Y=0.02688117 Z=0.92345027
  MULT= 4  ISPLIT= 8
  -7: X=0.27021191 Y=0.47311883 Z=0.07654973
  -7: X=0.22978809 Y=0.52688117 Z=0.57654973
  -7: X=0.72978809 Y=0.97311883 Z=0.42345027
C  NPT=  781  R0=.00010 RMT=   1.0   Z:   6.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -8: X=0.71430005 Y=0.93775232 Z=0.02930031
  MULT= 4  ISPLIT= 8
  -8: X=0.21430005 Y=0.56224768 Z=0.97069969
  -8: X=0.28569995 Y=0.43775232 Z=0.47069969
  -8: X=0.78569995 Y=0.06224768 Z=0.52930031
C  NPT=  781  R0=.00010 RMT=   1.0   Z:   6.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -9: X=0.95793250 Y=0.97413828 Z=0.89641001
  MULT= 4  ISPLIT= 8
  -9: X=0.45793250 Y=0.52586172 Z=0.10358999
  -9: X=0.04206750 Y=0.47413828 Z=0.60358999
  -9: X=0.54206750 Y=0.02586172 Z=0.39641001
C  NPT=  781  R0=.00010 RMT=   1.0   Z:   6.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.

Re: [Wien] an error from lapw1 I cannot get rid of (whatever I do !)

2013-09-13 Thread Fabiana Da Pieve

Dear Professor Marks

you are totally right , now it seems to work.

(sorry, I forgot to say that obviously I also tried different Rkmax
values5.5,5.0,4.5,6.0, with Gmax always 24 , number of kpoints I
tried: 1000, 1200, 1600, 2000)...
I tried everything ...

Thank you very much !
Fabiana

VUB, Brussels










2013/9/13, Laurence Marks :
> The most obvious thing to start is that the angles should be 90.0
> exactly, and the translations at the bottom should be 0. (do x
> patchsymm). Without this there could be problems.
>
> Beyond that I don't see anything obvious. You have not said what RKMAX
> etc you are using, so I don't think we can suggest much more.
>
> N.B., I noticed that xx does not have a BVS for N-H. If someone would
> like to do the mini project of adding it that would be useful to
> others.
>
> On Fri, Sep 13, 2013 at 9:37 AM, Fabiana Da Pieve
>  wrote:
>> Dear Wien2k developers and users
>>
>> now you will kill me because on this question there are already many
>> things in the mailing list.
>> I have tried everything possible for this compound (structure file
>> below) and I yet I did not succeed to make the scf run properly.
>>
>> I get the error:
>> Error in LAPW1
>>  'SELECT' - no energy limits found for L= 0
>>  'SELECT' - E-bottom -200.0   E-top   -5.68200
>>
>> I have tried to: reduce Rmt, change the number of k points, change the
>> mixing factor, change the energy parameters everything that was
>> suggested in the mailing list and other things that I found on the
>> userguide. But there is no way ! I failed.
>>
>> The strange thing is that I am running many other similar compounds,
>> and I never had any problems (really, they are very similar
>> compounds).
>>
>> All suggestions are very much appreciated
>>
>> Thank you very much for your attention
>> Fabiana
>>
>>
>>
>> Wien97 struct file generated by XCrySDen program
>> P   20
>>  NREL
>>  14.886988 13.751427 23.899435 90.01 90.01 90.01
>> ATOM  -1: X=0.46745645 Y=0.13407779 Z=0.72177357
>>   MULT= 4  ISPLIT= 8
>>   -1: X=0.96745645 Y=0.36592221 Z=0.27822643
>>   -1: X=0.53254355 Y=0.63407779 Z=0.77822643
>>   -1: X=0.03254355 Y=0.86592221 Z=0.22177357
>> O  NPT=  781  R0=.00010 RMT=   1.2   Z:   8.0
>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>  0.000 1.000 0.000
>>  0.000 0.000 1.000
>> ATOM  -2: X=0.82401610 Y=0.34963726 Z=0.99052607
>>   MULT= 4  ISPLIT= 8
>>   -2: X=0.32401610 Y=0.15036274 Z=0.00947393
>>   -2: X=0.17598390 Y=0.84963726 Z=0.50947393
>>   -2: X=0.67598390 Y=0.65036274 Z=0.49052607
>> O  NPT=  781  R0=.00010 RMT=   1.2   Z:   8.0
>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>  0.000 1.000 0.000
>>  0.000 0.000 1.000
>> ATOM  -3: X=0.65523123 Y=0.98268849 Z=0.83813124
>>   MULT= 4  ISPLIT= 8
>>   -3: X=0.15523123 Y=0.51731151 Z=0.16186876
>>   -3: X=0.34476877 Y=0.48268849 Z=0.66186876
>>   -3: X=0.84476877 Y=0.01731151 Z=0.33813124
>> N  NPT=  781  R0=.00010 RMT=   1.2   Z:   7.0
>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>  0.000 1.000 0.000
>>  0.000 0.000 1.000
>> ATOM  -4: X=0.63997780 Y=0.28559270 Z=0.84768142
>>   MULT= 4  ISPLIT= 8
>>   -4: X=0.13997780 Y=0.21440730 Z=0.15231858
>>   -4: X=0.36002220 Y=0.78559270 Z=0.65231858
>>   -4: X=0.86002220 Y=0.71440730 Z=0.34768142
>> N  NPT=  781  R0=.00010 RMT=   1.2   Z:   7.0
>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>  0.000 1.000 0.000
>>  0.000 0.000 1.000
>> ATOM  -5: X=0.57914808 Y=0.13124269 Z=0.79711804
>>   MULT= 4  ISPLIT= 8
>>   -5: X=0.07914808 Y=0.36875731 Z=0.20288196
>>   -5: X=0.42085192 Y=0.63124269 Z=0.70288196
>>   -5: X=0.92085192 Y=0.86875731 Z=0.29711804
>> C  NPT=  781  R0=.00010 RMT=   1.0   Z:   6.0
>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>  0.000 1.000 0.000
>>  0.000 0.000 1.000
>> ATOM  -6: X=0.75040671 Y=0.23930188 Z=0.92730470
>>

Re: [Wien] an error from lapw1 I cannot get rid of (whatever I do !)

2013-09-13 Thread Fabiana Da Pieve

yes I know it's high

but I am comparing the TB-mBJ with GW, and I want to be sure of having
used quite large parameters for the calculations with wien2k. Also my
Rkmax could probably be reduced.

(truth: I started this study, which is on several compounds, with 1000
kpoints, and now I am stuck with 1000 kpoints   :/ )

Thanks again !
F.







2013/9/13, Laurence Marks :
> Glad my guess worked.
>
> Considering the size of your cell, 1000 is a very large number of
> k-points particularly if it is an insulator.
>
> On Fri, Sep 13, 2013 at 10:54 AM, Fabiana Da Pieve
>  wrote:
>> Dear Professor Marks
>>
>> you are totally right , now it seems to work.
>>
>> (sorry, I forgot to say that obviously I also tried different Rkmax
>> values5.5,5.0,4.5,6.0, with Gmax always 24 , number of kpoints I
>> tried: 1000, 1200, 1600, 2000)...
>> I tried everything ...
>>
>> Thank you very much !
>> Fabiana
>>
>> VUB, Brussels
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 2013/9/13, Laurence Marks :
>>> The most obvious thing to start is that the angles should be 90.0
>>> exactly, and the translations at the bottom should be 0. (do x
>>> patchsymm). Without this there could be problems.
>>>
>>> Beyond that I don't see anything obvious. You have not said what RKMAX
>>> etc you are using, so I don't think we can suggest much more.
>>>
>>> N.B., I noticed that xx does not have a BVS for N-H. If someone would
>>> like to do the mini project of adding it that would be useful to
>>> others.
>>>
>>> On Fri, Sep 13, 2013 at 9:37 AM, Fabiana Da Pieve
>>>  wrote:
>>>> Dear Wien2k developers and users
>>>>
>>>> now you will kill me because on this question there are already many
>>>> things in the mailing list.
>>>> I have tried everything possible for this compound (structure file
>>>> below) and I yet I did not succeed to make the scf run properly.
>>>>
>>>> I get the error:
>>>> Error in LAPW1
>>>>  'SELECT' - no energy limits found for L= 0
>>>>  'SELECT' - E-bottom -200.0   E-top   -5.68200
>>>>
>>>> I have tried to: reduce Rmt, change the number of k points, change the
>>>> mixing factor, change the energy parameters everything that was
>>>> suggested in the mailing list and other things that I found on the
>>>> userguide. But there is no way ! I failed.
>>>>
>>>> The strange thing is that I am running many other similar compounds,
>>>> and I never had any problems (really, they are very similar
>>>> compounds).
>>>>
>>>> All suggestions are very much appreciated
>>>>
>>>> Thank you very much for your attention
>>>> Fabiana
>>>>
>>>>
>>>>
>>>> Wien97 struct file generated by XCrySDen program
>>>> P   20
>>>>  NREL
>>>>  14.886988 13.751427 23.899435 90.01 90.01 90.01
>>>> ATOM  -1: X=0.46745645 Y=0.13407779 Z=0.72177357
>>>>   MULT= 4  ISPLIT= 8
>>>>   -1: X=0.96745645 Y=0.36592221 Z=0.27822643
>>>>   -1: X=0.53254355 Y=0.63407779 Z=0.77822643
>>>>   -1: X=0.03254355 Y=0.86592221 Z=0.22177357
>>>> O  NPT=  781  R0=.00010 RMT=   1.2   Z:   8.0
>>>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>>>  0.000 1.000 0.000
>>>>  0.000 0.000 1.000
>>>> ATOM  -2: X=0.82401610 Y=0.34963726 Z=0.99052607
>>>>   MULT= 4  ISPLIT= 8
>>>>   -2: X=0.32401610 Y=0.15036274 Z=0.00947393
>>>>   -2: X=0.17598390 Y=0.84963726 Z=0.50947393
>>>>   -2: X=0.67598390 Y=0.65036274 Z=0.49052607
>>>> O  NPT=  781  R0=.00010 RMT=   1.2   Z:   8.0
>>>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>>>  0.000 1.000 0.000
>>>>  0.000 0.000 1.000
>>>> ATOM  -3: X=0.65523123 Y=0.98268849 Z=0.83813124
>>>>   MULT= 4  ISPLIT= 8
>>>>   -3: X=0.15523123 Y=0.51731151 Z=0.16186876
>>>>   -3: X=0.34476877 Y=0.48268849 Z=0.66186876
>>>>   -3: X=0.84476877 Y=0.01731151 Z=0.33813124
>>>> N

[Wien] restarting the TB-mBJ with a bigger mixing to speed up calculations

2013-09-16 Thread Fabiana Da Pieve

Dear Wien2k developers

I have a very simple technical question on TB-mBJ calculations. I
cannot allow myself to make any error as my contract runs only until
the end of the month.

I am running TB-mBJ calculations to be compared with GW. Doing "grep
GAP *scf* " inside my TB-mBJ directory, I see that the calculation is
proceeding well, the band gap is increasing, pretty going towards
convergence and pretty going towards the GW result ;
The command I am using for running such calculation is:
run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100

I have always obtained good results with such convergence criteria
compared to experiments and to predictions from other (non
all-electron) codes using PAW.

however, if I do " grep :ENE *scf* "  in such TB-mBJ directory, the
total energy does not really seems to go towards convergence, or
anyway it is too slow for the remaining time I have (but the energy
does NOT oscillate, or diverge, which is good).

>From the usersguide (I am using wien2k-11), I see that it is advised
to change at a certain point from a mixing factor 0.2 (the one I am
using now) to 0.5 (which should increase the speed).

Could you please tell me the DETAILED instructions to abort the
calculation and restart it without breaking ANYTHING (i.e. restarting
safely the calculations with mixing 0.5, from the very last scf step
with mixing 0.2 completed before I kill my calculation) ??

Thank you very much in advance

Fabiana
VUB, Free University of Brussels
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Re: [Wien] restarting the TB-mBJ with a bigger mixing to speed up calculations

2013-09-16 Thread Fabiana Da Pieve

Dear Dr. Tran

thank you very much for your answer. Well, I am not only interested in
the gap, I want to check the performance of TB-mBJ also for the width
of the valence and conduction region with respect to GW. So, I want to
calculate the TB-mBJ band structure when my TB-mBJ SCF calculations is
finished, to be compared with the GW band structure obtained by
Wannierization.

So, if I understand well, these are the things I have to do:
- inside my directory "touch .stop"
- I do not need to send "qdel" or "scancel" to the scheduler of my
cluster, the code will detect the .stop file and automatically stops
when the current iteration is finished. Right ?
- When it has stopped, I change the mixing in case.inm to 0.5
- I restart the calculation with my command
  run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100

ARE YOU SURE THAT THIS COMMAND DOES NOT NEED ANY MODIFICATION ?
 (sorry, but I really cannot allow myself to make any error)

Thank you very much

Fabiana





2013/9/16, t...@theochem.tuwien.ac.at :
> Hi,
>
> to stop a calculation properly you have to create a .stop file
> (with "touch .stop") in the directory of your calculation. Wien2k
> will detect this file and stop the calculation a the end of the current
> iteration. Then, modify case.inm and restart the calculation as before.
>
> With mBJ, the energy converges very slowly, but does not diverge.
> If you think that :GAP is converged (and this is the only quantity that
> you need), maybe you don't really need to converge :ENE.
>
> F. Tran
>
> On Mon, 16 Sep 2013, Fabiana Da Pieve wrote:
>
>> Dear Wien2k developers
>>
>> I have a very simple technical question on TB-mBJ calculations. I
>> cannot allow myself to make any error as my contract runs only until
>> the end of the month.
>>
>> I am running TB-mBJ calculations to be compared with GW. Doing "grep
>> GAP *scf* " inside my TB-mBJ directory, I see that the calculation is
>> proceeding well, the band gap is increasing, pretty going towards
>> convergence and pretty going towards the GW result ;
>> The command I am using for running such calculation is:
>> run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100
>>
>> I have always obtained good results with such convergence criteria
>> compared to experiments and to predictions from other (non
>> all-electron) codes using PAW.
>>
>> however, if I do " grep :ENE *scf* "  in such TB-mBJ directory, the
>> total energy does not really seems to go towards convergence, or
>> anyway it is too slow for the remaining time I have (but the energy
>> does NOT oscillate, or diverge, which is good).
>>
>>> From the usersguide (I am using wien2k-11), I see that it is advised
>> to change at a certain point from a mixing factor 0.2 (the one I am
>> using now) to 0.5 (which should increase the speed).
>>
>> Could you please tell me the DETAILED instructions to abort the
>> calculation and restart it without breaking ANYTHING (i.e. restarting
>> safely the calculations with mixing 0.5, from the very last scf step
>> with mixing 0.2 completed before I kill my calculation) ??
>>
>> Thank you very much in advance
>>
>> Fabiana
>> VUB, Free University of Brussels
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Re: [Wien] restarting the TB-mBJ with a bigger mixing to speed up calculations

2013-09-16 Thread Fabiana Da Pieve

ok, thank you very much !

Fabiana


2013/9/16, t...@theochem.tuwien.ac.at :
> It should be ok.
>
> On Mon, 16 Sep 2013, Fabiana Da Pieve wrote:
>
>> Dear Dr. Tran
>>
>> thank you very much for your answer. Well, I am not only interested in
>> the gap, I want to check the performance of TB-mBJ also for the width
>> of the valence and conduction region with respect to GW. So, I want to
>> calculate the TB-mBJ band structure when my TB-mBJ SCF calculations is
>> finished, to be compared with the GW band structure obtained by
>> Wannierization.
>>
>> So, if I understand well, these are the things I have to do:
>> - inside my directory "touch .stop"
>> - I do not need to send "qdel" or "scancel" to the scheduler of my
>> cluster, the code will detect the .stop file and automatically stops
>> when the current iteration is finished. Right ?
>> - When it has stopped, I change the mixing in case.inm to 0.5
>> - I restart the calculation with my command
>>  run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100
>>
>> ARE YOU SURE THAT THIS COMMAND DOES NOT NEED ANY MODIFICATION ?
>> (sorry, but I really cannot allow myself to make any error)
>>
>> Thank you very much
>>
>> Fabiana
>>
>>
>>
>>
>>
>> 2013/9/16, t...@theochem.tuwien.ac.at :
>>> Hi,
>>>
>>> to stop a calculation properly you have to create a .stop file
>>> (with "touch .stop") in the directory of your calculation. Wien2k
>>> will detect this file and stop the calculation a the end of the current
>>> iteration. Then, modify case.inm and restart the calculation as before.
>>>
>>> With mBJ, the energy converges very slowly, but does not diverge.
>>> If you think that :GAP is converged (and this is the only quantity that
>>> you need), maybe you don't really need to converge :ENE.
>>>
>>> F. Tran
>>>
>>> On Mon, 16 Sep 2013, Fabiana Da Pieve wrote:
>>>
>>>> Dear Wien2k developers
>>>>
>>>> I have a very simple technical question on TB-mBJ calculations. I
>>>> cannot allow myself to make any error as my contract runs only until
>>>> the end of the month.
>>>>
>>>> I am running TB-mBJ calculations to be compared with GW. Doing "grep
>>>> GAP *scf* " inside my TB-mBJ directory, I see that the calculation is
>>>> proceeding well, the band gap is increasing, pretty going towards
>>>> convergence and pretty going towards the GW result ;
>>>> The command I am using for running such calculation is:
>>>> run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100
>>>>
>>>> I have always obtained good results with such convergence criteria
>>>> compared to experiments and to predictions from other (non
>>>> all-electron) codes using PAW.
>>>>
>>>> however, if I do " grep :ENE *scf* "  in such TB-mBJ directory, the
>>>> total energy does not really seems to go towards convergence, or
>>>> anyway it is too slow for the remaining time I have (but the energy
>>>> does NOT oscillate, or diverge, which is good).
>>>>
>>>>> From the usersguide (I am using wien2k-11), I see that it is advised
>>>> to change at a certain point from a mixing factor 0.2 (the one I am
>>>> using now) to 0.5 (which should increase the speed).
>>>>
>>>> Could you please tell me the DETAILED instructions to abort the
>>>> calculation and restart it without breaking ANYTHING (i.e. restarting
>>>> safely the calculations with mixing 0.5, from the very last scf step
>>>> with mixing 0.2 completed before I kill my calculation) ??
>>>>
>>>> Thank you very much in advance
>>>>
>>>> Fabiana
>>>> VUB, Free University of Brussels
>>>> ___
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>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
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>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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Re: [Wien] restarting the TB-mBJ with a bigger mixing to speed up calculations

2013-09-16 Thread Fabiana Da Pieve

ok, yes I think I will do like this !

Thank you very much for the suggestion

Fabiana

2013/9/16, Laurence Marks :
> The user guide says that you should be able to switch back to MSR1, which
> should be faster than using PRATT. In that case the mixing greed does not
> matter and you can leave it at 0.2.
>
> ---
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu 1-847-491-3996
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought"
> Albert Szent-Gyorgi
>  On Sep 16, 2013 4:45 AM, "Fabiana Da Pieve" 
> wrote:
>
>> ok, thank you very much !
>>
>> Fabiana
>>
>>
>> 2013/9/16, t...@theochem.tuwien.ac.at :
>> > It should be ok.
>> >
>> > On Mon, 16 Sep 2013, Fabiana Da Pieve wrote:
>> >
>> >> Dear Dr. Tran
>> >>
>> >> thank you very much for your answer. Well, I am not only interested in
>> >> the gap, I want to check the performance of TB-mBJ also for the width
>> >> of the valence and conduction region with respect to GW. So, I want to
>> >> calculate the TB-mBJ band structure when my TB-mBJ SCF calculations is
>> >> finished, to be compared with the GW band structure obtained by
>> >> Wannierization.
>> >>
>> >> So, if I understand well, these are the things I have to do:
>> >> - inside my directory "touch .stop"
>> >> - I do not need to send "qdel" or "scancel" to the scheduler of my
>> >> cluster, the code will detect the .stop file and automatically stops
>> >> when the current iteration is finished. Right ?
>> >> - When it has stopped, I change the mixing in case.inm to 0.5
>> >> - I restart the calculation with my command
>> >>  run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100
>> >>
>> >> ARE YOU SURE THAT THIS COMMAND DOES NOT NEED ANY MODIFICATION ?
>> >> (sorry, but I really cannot allow myself to make any error)
>> >>
>> >> Thank you very much
>> >>
>> >> Fabiana
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> 2013/9/16, t...@theochem.tuwien.ac.at :
>> >>> Hi,
>> >>>
>> >>> to stop a calculation properly you have to create a .stop file
>> >>> (with "touch .stop") in the directory of your calculation. Wien2k
>> >>> will detect this file and stop the calculation a the end of the
>> >>> current
>> >>> iteration. Then, modify case.inm and restart the calculation as
>> >>> before.
>> >>>
>> >>> With mBJ, the energy converges very slowly, but does not diverge.
>> >>> If you think that :GAP is converged (and this is the only quantity
>> >>> that
>> >>> you need), maybe you don't really need to converge :ENE.
>> >>>
>> >>> F. Tran
>> >>>
>> >>> On Mon, 16 Sep 2013, Fabiana Da Pieve wrote:
>> >>>
>> >>>> Dear Wien2k developers
>> >>>>
>> >>>> I have a very simple technical question on TB-mBJ calculations. I
>> >>>> cannot allow myself to make any error as my contract runs only until
>> >>>> the end of the month.
>> >>>>
>> >>>> I am running TB-mBJ calculations to be compared with GW. Doing "grep
>> >>>> GAP *scf* " inside my TB-mBJ directory, I see that the calculation
>> >>>> is
>> >>>> proceeding well, the band gap is increasing, pretty going towards
>> >>>> convergence and pretty going towards the GW result ;
>> >>>> The command I am using for running such calculation is:
>> >>>> run_lapw -p -I -cc 0.001 -ec 0.0001 -it -i 100
>> >>>>
>> >>>> I have always obtained good results with such convergence criteria
>> >>>> compared to experiments and to predictions from other (non
>> >>>> all-electron) codes using PAW.
>> >>>>
>> >>>> however, if I do " grep :ENE *scf* "  in such TB-mBJ directory, the
>> >>>> total energy does not really seems to go towards convergence, or
>> >>>> anyway it is too slow for the remaining time I have (but the energy
>> >>>> does NOT oscil

[Wien] how to start an mBJ after a GGA calculation of the band structure and an unexplicable error

2013-10-02 Thread Fabiana Da Pieve

Dear Wien2k developers

I am continuing my Tran-Blaha mBJ studies on a series of crystals, and
most of them are proceeding fine (one has finished and compares well
with GW).
However, for one of them, I have a problem. I have two different sets
of calculations for it:

1) one is done with quite high parameters (only at the GGA level) and
it worked fine, I did the usual things (SCF,DOS and band structure).

2) Then I wanted to do the TB-mBJ, and I decided to RE-run (in a
different directory) the preparatory GGA SCF cycle with lower
parameters with respect to case 1). I do not know why, but this time
the GGA runs fails, with the messages in the dayfile and in the error
file that I report below. I have tried to re-initialize the
calculation and re-run the calculation several times, but it always
fails. Why it fails and why before it was working is unexplicable to
me !!

So: I said to myself, ok, let's forget about this "low parameters"
calculation and let's run the mBJ on the very initial GGA run (with
high parameters). However, in this directory I have calculated, as I
said before, the GGA DOS and the GGA band structure, exactly in this
order. The GGA band structure is done on a different number of k
points with respect to the initial GGA SCF run.

How can I start now an mBJ calculation in this directory ?
Do I have to regenerate the klist file, as it was for the initial GGA
run, and then maybe relaunch lapw1, before doing all the preparatory
steps for the mBJ (i.e. create case.inm_vresp, set r2v in case.in0 and
do run_lapw -NI -i 1) ???
(if you could explain things step by step it would be very helpful for me)

Thank you very much for your help and patience
Fabiana

These are the errors I get for the "low parameters" GGA SCF run:

in thedayfile:

>   lapw2 -p(02:59:27) running LAPW2 in parallel mode
**  LAPW2 crashed!
error: command   /data/home/lamoen/wien2k-11/lapw2para lapw2.def   failed
>   stop error

and the message in the error file:

cp: cannot stat `.in.tmp': No such file or directory
rm: cannot remove `.in.tmp': No such file or directory
rm: cannot remove `.in.tmp1': No such file or directory
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Re: [Wien] how to start an mBJ after a GGA calculation of the band structure and an unexplicable error

2013-10-02 Thread Fabiana Da Pieve

Dear Prof. /Dr. Tran

Thank you very much for your answer.
Yes indeed you are right, if the klist file is the one related to the
SCF GGA run I should be able to start the mBJ run without problems.
I was confused by the idea that , since I also calculated the band
structure in that directory (with a different number of k point with
respect tot he SCF GGA run), the klist file now could have been
different from the one of the SCF GGA run.
But actually these "kilst" files for the SCF and the band structure
calculation are named differently !! (indeed the klist file for the
band structure, when it is generated, it is actually generated as
klist_band)

Thanks a lot !
Fabiana





2013/10/2, t...@theochem.tuwien.ac.at :
> I don't know what can be the problem in your "low parameters"
> directory, but maybe a "clean_lapw" or running on another machine
> can help.
>
> In your "high parameters" directory, if case.klist is the proper
> file then you can do the preparatory steps for the mBJ as usual.
>
> F. Tran
>
> On Wed, 2 Oct 2013, Fabiana Da Pieve wrote:
>
>> Dear Wien2k developers
>>
>> I am continuing my Tran-Blaha mBJ studies on a series of crystals, and
>> most of them are proceeding fine (one has finished and compares well
>> with GW).
>> However, for one of them, I have a problem. I have two different sets
>> of calculations for it:
>>
>> 1) one is done with quite high parameters (only at the GGA level) and
>> it worked fine, I did the usual things (SCF,DOS and band structure).
>>
>> 2) Then I wanted to do the TB-mBJ, and I decided to RE-run (in a
>> different directory) the preparatory GGA SCF cycle with lower
>> parameters with respect to case 1). I do not know why, but this time
>> the GGA runs fails, with the messages in the dayfile and in the error
>> file that I report below. I have tried to re-initialize the
>> calculation and re-run the calculation several times, but it always
>> fails. Why it fails and why before it was working is unexplicable to
>> me !!
>>
>> So: I said to myself, ok, let's forget about this "low parameters"
>> calculation and let's run the mBJ on the very initial GGA run (with
>> high parameters). However, in this directory I have calculated, as I
>> said before, the GGA DOS and the GGA band structure, exactly in this
>> order. The GGA band structure is done on a different number of k
>> points with respect to the initial GGA SCF run.
>>
>> How can I start now an mBJ calculation in this directory ?
>> Do I have to regenerate the klist file, as it was for the initial GGA
>> run, and then maybe relaunch lapw1, before doing all the preparatory
>> steps for the mBJ (i.e. create case.inm_vresp, set r2v in case.in0 and
>> do run_lapw -NI -i 1) ???
>> (if you could explain things step by step it would be very helpful for
>> me)
>>
>> Thank you very much for your help and patience
>> Fabiana
>>
>> These are the errors I get for the "low parameters" GGA SCF run:
>>
>> in thedayfile:
>>
>>>   lapw2 -p(02:59:27) running LAPW2 in parallel mode
>> **  LAPW2 crashed!
>> error: command   /data/home/lamoen/wien2k-11/lapw2para lapw2.def   failed
>>>   stop error
>>
>> and the message in the error file:
>>
>> cp: cannot stat `.in.tmp': No such file or directory
>> rm: cannot remove `.in.tmp': No such file or directory
>> rm: cannot remove `.in.tmp1': No such file or directory
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Re: [Wien] DFT in biomedical research

2021-03-10 Thread Fabiana Da Pieve

Dear Prof. Marks

I am coordinating an European project where we are using DFT/TDDFT to study
the impact of ions in biological matter, of importance for radiation
biology and biomedical research. But we are *NOT* studying any particular
material of practical use in biomedical research.

Fabiana





Il giorno mer 10 mar 2021 alle ore 14:45 Laurence Marks <
laurence.ma...@gmail.com> ha scritto:

> I realize this is not really a W2k question, but anyway: is anyone aware
> of much use of DFT in biomedical research?
>
> _
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
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Re: [Wien] DFT in biomedical research

2021-03-10 Thread Fabiana Da Pieve

 In reference to the email from Suxing, some attention should be paid to
the words "energetic particles"

It is actually more the speed of the particle, rather than the energy, that
counts for the relevance of the applicability of electronic structure
methods in the field of ion irradiation.

For energetic light ions (from few tenths of Mev to higher) impacting on
biomaterials, one absolutely does NOT need DFT, as the impacting particle
will not be sensitive to the electronic structure details of the target.
If the light ion is slow (so, the speed is low, and energy is below some
few MeV), then the electronic and geometrical details of the target maye
play a role (I would say starting from few hundreds keV, even less)

If the "energetic particle" is a heavy ion, then its energy may be mostly
due to the mass. It could  actually be a slow big ion. In the case of such
a low speed big ion, with high energy, then one would indeed be sensitive
again to the details of the target. If the heavy ion is very energetic also
because it has high speed, then again DFT methods are not of relevance.

Il giorno mer 10 mar 2021 alle ore 15:44 Michael Sluydts <
michael.sluy...@ugent.be> ha scritto:

> Hey Laurence,
>
> Not sure if you're specifically thinking of solid-state, but typical
> biochemistry applications are common.
>
> For instance DFT and AI for drug discovery:
>
> https://www.technologyreview.com/10-breakthrough-technologies/2020/#ai-discovered-molecules
>
> Studies of initial polymer reactions, functional groups of proteins and so
> on also spring to mind or to try and get dynamic properties/spectroscopy of
> (parts of) very small proteins.
>
> In the end also DFT components to make forcefields or machine learning
> potentials for all kinds of applications are also very relevant nowadays
> (by sampling subsystems of larger ones).
> Colleague of mine used to study oxygen transport in lipid membranes with
> the NIH, not ab initio MD, but i can imagine the ML potential approach may
> be interesting.
>
> https://molmod.ugent.be/publications/permeability-membranes-liquid-ordered-and-liquid-disordered-phases
>
> Just some quick thoughts though. ;)
>
> Kind regards,
>
> Michael Sluydts
>
> On 3/10/2021 2:45 PM, Laurence Marks wrote:
>
> I realize this is not really a W2k question, but anyway: is anyone aware
> of much use of DFT in biomedical research?
>
> _
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
>
> ___
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>
> --
> dr. ir. Michael Sluydts
> Center for Molecular Modeling
> Ghent University
> Technologiepark 903
> 9052 Zwijnaarde, Belgium
> tel. +32 (0)9 264 66 19https://molmod.ugent.be
>
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[Wien] my membership to the mailing list gets disabled every 3 weeks

2017-01-30 Thread Fabiana Da Pieve

Dear Wien2k developers

I am a pretty silent user of Wien2k since many years and I always read with
pleasure the emails of the different users, which sometimes are also useful
for me.

However, in the last period I get very often (every 3 weeks) an email to
confirm my membership to the mailing list, and if I do not do it soon my
membership is cancelled the very same day.

I do not think this is normal. Or is it ?
In any case, before it was not the case. Is there something I can do to
avoid this ?

Thank you very much for your attention
Fabiana Da Pieve
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Re: [Wien] my membership to the mailing list gets disabled every 3 weeks

2017-01-30 Thread Fabiana Da Pieve

Dear Prof. Blaha

I have checked my spam inbox and no, none of the email that my gmail
account automatically archived as spam was coming from Wien2k, in THIS last
period.

However, in the past sometimes it has happened , that's true, that I have
found some emails from Wien2k in the spam box (one, or two over more than
one hundred spam email).
But considering that I am lazy in empting my spam inbox, those one/two
emails over more than one hundred were corresponding to a period that was
spanning more than 3 weeks.

So, strange that 5 or 10 bounces are generated in a period of 3 weeks
(which is the frequency with which I have to renew the membership).

In any case, the problem is not only detected by those who have a gmail
account (lyudmila has mail.ru)

Thanks for your attention
Fabiana



2017-01-30 16:49 GMT+01:00 Luis Ogando :

> Dear Prof. Blaha,
>
>Unfortunately, I am facing the same problem described by Dr. Fabiana Da
> Pieve.
>Please, let me know if I can do anything to help.
>All the best,
>   Luis
>
>
> 2017-01-30 13:34 GMT-02:00 Peter Blaha :
>
>> I've nothing changed recently in the mailing list configuration, so I
>> don't know why this should now happen (except when your mail system has
>> changed e.g spam-processing, ...)
>>
>> It probably comes from   bounce processing, i.e. mailman cannot send to
>> your email addresses and gets a bounce back. After 5 (or 10 days if it is a
>> soft bounce) it will disable your membership and just before, it will send
>> you a warning.
>>
>> It may have to do with your specific email accounts ? maybe they think it
>> is spam ... ?
>>
>> Of course, I can increase the bounce level from 5 (up to 10), but for
>> sure I want to keep it, otherwise mailman will keep outdated addresses
>> forever and continues to send mails to them.
>>
>> Regards
>>
>> Am 30.01.2017 um 09:26 schrieb Fabiana Da Pieve:
>>
>>> Dear Wien2k developers
>>>
>>> I am a pretty silent user of Wien2k since many years and I always read
>>> with pleasure the emails of the different users, which sometimes are
>>> also useful for me.
>>>
>>> However, in the last period I get very often (every 3 weeks) an email to
>>> confirm my membership to the mailing list, and if I do not do it soon my
>>> membership is cancelled the very same day.
>>>
>>> I do not think this is normal. Or is it ?
>>> In any case, before it was not the case. Is there something I can do to
>>> avoid this ?
>>>
>>> Thank you very much for your attention
>>> Fabiana Da Pieve
>>>
>>>
>>>
>>>
>>> ___
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>>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>>> e...@zeus.theochem.tuwien.ac.at/index.html
>>>
>>>
>> --
>> 
>> --
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
>> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
>> 
>> --
>> ___
>> Wien mailing list
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>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wi
>> e...@zeus.theochem.tuwien.ac.at/index.html
>>
>
>
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[Wien] hybrids + vdW

2017-05-16 Thread Fabiana Da Pieve

Dear Wien2k developers

I have some simple questions before I start some new calculations:

- is it possible to relax a structure with YS-PBE0 or HSE06, adding also
simultaneously van der Waals corrections via the Grimme D3 method ?

- if I understand well, one CANNOT relax a structure when considering mBJ.
This sounds reasonable as I expect that forces and stresses are not
calculated when considering the potential mBJ. Please correct me if I am
wrong. I got a bit confused by a post this morning.

- I guess it is anyway possible to run an SCF mBJ calculation (adding
simultaneously the vdW via the D3 method) to further extract the band
structure , on a structure that has been indeed PREVIOUSLY relaxed via
combining YS-PBE0 (or HSE06) +D3. I guess the answer is yes, **please
correct me in case I am wrong**.
I have anyway some doubt about the adding of the D3 corrections. I am not
really sure all this would make a sense, from the point of view of
correctly considering vdW corrections in a consistent way.
Is there a comment you might want to add ?

Thank you very much in advance for your attention
F.
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Re: [Wien] hybrids + vdW

2017-05-16 Thread Fabiana Da Pieve

Dear Dr. Tran,

thank you very much for your answer.

Fabiana

2017-05-16 16:57 GMT+02:00 :

> Hi,
>
> In WIEN2k the forces are implemented for LDA/GGA and LDA/GGA+D3, but not
> for MGGA and hybrid. So, no relaxation of atomic positions
> with MGGA and hybrid.
>
> mBJ is not a functional derivative such that it is theoretically
> impossible to define forces which have a physical meaning.
>
> If the only way to relax atomic positions is with forces
> (too complicated to do it "manually"), then you need to use
> GGA or GGA+D3. Then, use hybrid or mBJ at the optimized
> geometry for the electronic structure.
>
> The stress tensor is not implemented in WIEN2k.
>
> FT
>
> On Tuesday 2017-05-16 16:28, Fabiana Da Pieve wrote:
>
> Date: Tue, 16 May 2017 16:28:35
>> From: Fabiana Da Pieve 
>> Reply-To: A Mailing list for WIEN2k users > at>
>> To: A Mailing list for WIEN2k users 
>> Subject: [Wien] hybrids + vdW
>>
>>
>> Dear Wien2k developers
>>
>> I have some simple questions before I start some new calculations:
>>
>> - is it possible to relax a structure with YS-PBE0 or HSE06, adding also
>> simultaneously van der Waals corrections via the Grimme D3 method ?
>>
>> - if I understand well, one CANNOT relax a structure when considering mBJ.
>> This sounds reasonable as I expect that forces and stresses are not
>> calculated when considering the potential mBJ. Please correct me if I am
>> wrong. I got a bit confused by a post this morning.
>>
>> - I guess it is anyway possible to run an SCF mBJ calculation (adding
>> simultaneously the vdW via the D3 method) to further extract the band
>> structure , on a structure that has been indeed PREVIOUSLY relaxed via
>> combining YS-PBE0 (or HSE06) +D3. I guess
>> the answer is yes, **please correct me in case I am wrong**.
>> I have anyway some doubt about the adding of the D3 corrections. I am not
>> really sure all this would make a sense, from the point of view of
>> correctly considering vdW corrections in a consistent way.
>> Is there a comment you might want to add ?
>>
>> Thank you very much in advance for your attention
>> F.
>>
>>
>>
>>
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Re: [Wien] hybrids + vdW

2017-05-16 Thread Fabiana Da Pieve

Dear Prof. Blaha,

thank you very much for this further comment !!

have a nice evening
F.


2017-05-16 18:00 GMT+02:00 Peter Blaha :

> Just to comment further on one point:
>
> - I guess it is anyway possible to run an SCF mBJ calculation (adding
>> simultaneously the vdW via the D3 method) to further extract the band
>> structure , on a structure that has been indeed PREVIOUSLY relaxed via
>> combining YS-PBE0 (or HSE06) +D3. I guess the answer is yes, **please
>> correct me in case I am wrong**.
>>
>
> "D3" has NO effect on the electronic eigenvalues (band structure). It is
> just an additional term to Etot (and to the forces acting on the atoms).
>
> --
>
>   P.Blaha
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/TC_Blaha
> --
>
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[Wien] papers published with Wien2k

2014-01-07 Thread Fabiana Da Pieve

Dear Wien2k developers


I totally forgot to say that in the last two years I have published two
(very simple, from what concerns my contribution) papers with Wien2k, in
collaboration with some experimentalists.


In the (likely, or unlikely, depends on you) case you want to add them on
the website of Wien2kthey are below.


more papers will come this year, hopefully.


Thank you very much to all the developers !


Fabiana Da Pieve




*Analysis of the Local Boron Environment in Boron-doped Nanocrystalline
Diamond Films, *

*S.Turner, Y. Lu, S. D. Janssens, F. Da Pieve, D. Lamoen, J. Verbeeck, K.
Haenen, P. Wagner and G. Van Tendeloo*


* Nanoscale 4, 5960 (2012)*

*Aberration-corrected microscopy and spectroscopy analysis of pristine and
nitrogen doped  detonation nanodiamond **
S. Turner, O. Shenderova, F. Da Pieve, E. Yücelen, D. Lamoen, J. Verbeeck
and G. Van Tendeloo**
Phys.Stat.Sol.(a), 210, 1976 (2013)  *
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Re: [Wien] papers published with Wien2k

2014-01-07 Thread Fabiana Da Pieve

Ops !!

thank you ! I did not notice there was such a tool...sorry.

Fabiana


2014/1/7 Masood Yousaf 

> Dear Tendeloo
>
> A short, quick and convenient way is to insert your publication through
> the fallowing form. After they will appear on the list soon.
>
> http://www.wien2k.at/papers/publ_input1.html
>
> Best wishes
> Masood
>
>
>   On Tuesday, January 7, 2014 11:17 PM, Fabiana Da Pieve <
> fabiana.dapi...@gmail.com> wrote:
>   Dear Wien2k developers
>
> I totally forgot to say that in the last two years I have published two
> (very simple, from what concerns my contribution) papers with Wien2k, in
> collaboration with some experimentalists.
>
> In the (likely, or unlikely, depends on you) case you want to add them on
> the website of Wien2kthey are below.
>
> more papers will come this year, hopefully.
>
> Thank you very much to all the developers !
>
> Fabiana Da Pieve
>
>
>
> *Analysis of the Local Boron Environment in Boron-doped Nanocrystalline
> Diamond Films, *
> *S.Turner, Y. Lu, S. D. Janssens, F. Da Pieve, D. Lamoen, J. Verbeeck, K.
> Haenen, P. Wagner and G. Van Tendeloo*
>
>
> * Nanoscale 4, 5960 (2012)*
> *Aberration-corrected microscopy and spectroscopy analysis of pristine and
> nitrogen doped  detonation nanodiamond **
> S. Turner, O. Shenderova, F. Da Pieve, E. Yücelen, D. Lamoen, J. Verbeeck
> and G. Van Tendeloo**
> Phys.Stat.Sol.(a), 210, 1976 (2013)  *
>
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>
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[Wien] exciton trapping

[Wien] exciton trapping

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Re: [Wien] the "c" parameter in TB-mBJ

[Wien] an error from lapw1 I cannot get rid of (whatever I do !)

Re: [Wien] an error from lapw1 I cannot get rid of (whatever I do !)

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Re: [Wien] restarting the TB-mBJ with a bigger mixing to speed up calculations

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[Wien] my membership to the mailing list gets disabled every 3 weeks

Re: [Wien] my membership to the mailing list gets disabled every 3 weeks

[Wien] hybrids + vdW

Re: [Wien] hybrids + vdW

Re: [Wien] hybrids + vdW

[Wien] papers published with Wien2k

Re: [Wien] papers published with Wien2k

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