Re: [QE-users] Master degree's student

[Matthieu Fortin-Deschênes]

I suggest that you start with the examples to get more familiar.

Matthieu

Abd-Elrahman Ali  a écrit :


Hello
Good day for you, Hope this Email finds you well,
I'd like to introduce myself to you as i am a new master degree student who
aim to study the metals- polymers interface using quantum espresso as a
tool to build my model and run it using super computers.
So i'd like to thank you for your effort which appear on the organization
in the website.
but i ask for more information and details about the input file parameters
as i cant understand most of the parameters although i read each word on
the website around these parameters and also study the manual guide but
still feeling there is a misunderstand of the input parameters of the input
file specially in the control and system part |
thanks in Advance

Abdelrahman Ali.
Teaching Assistant at Faculty of Engineering Cairo University
Electric power and machine Department
High Voltage Group




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Re: [QE-users] structural optimization

[Matthieu Fortin-Deschênes]

What errors?

These 3 seem wrong to me:

ibrav= 0,
celldm(1) = 1.44 ,
nat= 39,

Matthieu

Fedaa Nada  a écrit :

I am trying to do structure optimization for clusters of  
Ca3(PO4)2Here is my Input file but it gives me errors !?
 =  
'relax',restart_mode='from_scratch',prefix='POSNER',    pseudo_dir =  
'/home/fedaa/pslibrary/pbe/PSEUDOPOTENTIALS',outdir='/home/fedaa/molecules/POSNER' nstep=100 /= 0, celldm(1) = 1.44 ,nat= 39, ntyp= 3, ecutwfc = 29.39944706, occupation = 'smearing',smearing='mp'/_mode = 'plain'mixing_beta = 0.25conv_thr = 1.0d-8/_dynamics = 'bfgs'/_dynamics='bfgs'/ATOMIC_SPECIES Ca    40.077999 Ca.pbe-spn-kjpaw_psl.1.0.0.UPF P     30.973801  P.pbe-nl-kjpaw_psl.1.0.0.UPF O     15.999400  O.pbe-nl-kjpaw_psl.1.0.0.UPFATOMIC_POSITIONS {angstrom} Ca            5.331893237     3.078363839     3.945982462Ca            7.642749451     1.582212871     1.073672662Ca            2.880749721     1.825179137     1.073672662Ca            5.472164544     5.827708743     1.073672662Ca            7.587479101     4.196171199    10.73422Ca            3.236045403     4.472864052    10.73422Ca           -0.097498902     2.925273574     7.851053061Ca            5.172139211     0.566065501    10.73422Ca            7.616548553     4.080363035     6.428594062Ca            3.321803488     4.555943019     6.428594062Ca            2.847276128     7.688027439     7.851053061Ca           -2.749777226     7.856900491     7.851053061Ca            0.115078137     3.776832979     4.231584001Ca            5.057311674     0.598794698     6.428594062Ca           -2.118593668     7.247023672     4.231584001Ca            2.003515531     7.446344852     4.231584001Ca            5.527120313     6.758800836    12.961011258Ca            8.421620972     1.069073733    12.961011258Ca            2.046922431     1.407226182    12.961011258Ca            0.0     0.0    10.461753571Ca            0.0     0.0     3.116452421Ca           -0.05332     6.156736913    16.971077250Ca            2.310866877     4.660576710    14.098806526Ca           -2.451132853     4.903542976    14.098806526Ca            0.140281971     8.906072582    14.098806526Ca            2.255591196     7.274544273    23.580668210Ca           -2.095847834     7.551227891    23.580668210Ca            5.234389003     6.003646648    20.876147849Ca           -0.159743362     3.644429339    23.580668210Ca            2.284660648     7.158736109    19.453727925Ca           -2.010089749     7.634306858    19.453727925Ca            2.847270796     1.531290526    20.876147849Ca            7.914003916     1.700163578    20.876147849Ca            5.446966042     6.855206053    17.256717865Ca           -0.274570900     3.677158537    19.453727925Ca            8.545187474     1.090286760    17.256717865Ca            2.003510199     1.289607939    17.256717865Ca            5.527114981     0.602063923    25.986106046Ca            3.089733067     4.147446807    25.986106046Ca            7.378815667     4.485590021    25.986106046Ca            5.331893237     3.078363839    23.486848359Ca            5.331893237     3.078363839    16.141586285Ca            0.0     0.0    29.99624Ca           -3.021031691     7.738949784    27.123901314Ca            2.880744389     7.981916050    27.123901314Ca            0.140271307     2.749344904    27.123901314Ca            2.255585864     1.117807360    36.605802074Ca            8.567933308     1.394490978    36.605802074Ca           -0.097504234     9.082010487    33.901242637Ca            5.172144543     6.722802413    36.605802074Ca            2.284665980     1.001999196    32.478822713Ca            8.653691393     1.477569945    32.478822713Ca           -2.484611777     4.609654365    33.901242637Ca            2.582116011     4.778536652    33.901242637Ca            5.446971374     0.698469140    30.281812653Ca            5.057322337     6.755522375    32.478822713Ca            3.213294237     4.168650599    30.281812653Ca            7.335398104     4.367981013    30.281812653Ca            0.195227076     3.680436997    39.011239910Ca           -2.242149506     7.225810646    39.011239910Ca            2.046922431     7.563953860    39.011239910Ca           -0.05332     6.156736913    36.511943147Ca           -0.05332     6.156736913    29.166681073P             5.331887905     9.235100752     0.101947519P             8.155629080     1.170964600     5.205536438P             2.268158455     1.586636485     5.205536438P             5.571876180     6.477499667     5.205536438P            -0.148205156     3.254504916    11.641281284P             2.587501218     7.479508099    11.641281284P            -2.439312057     7.736197724    11.641281284P            -0.05332     6.156736913     6.487089821P             3.112206974     4.551270058     2.814947225P            -0.165731072     9.654716025     2.814947225P            -2.946475903     4.264215421     2.814947225P          

Re: [QE-users] Soft Hydrogen Pseudopotentials

[Matthieu Fortin-Deschênes]

Thanks for the info. I'll take a look at those papers.

Matthieu

Giuseppe Mattioli  a écrit :

I believe fractional charge H atoms would not be useful for these  
kinds of materials. Right?


I suppose you are right. I can only suggest you to double check the  
results and to carefully compare with experimental results obtained  
on real systems. I cited C-diamond, which is "akin" to Si and Ge,  
because surface hydrogenation induce a large upward shift of both  
valence and conduction bands, measured by ARPES and compared with  
DFT calculations here: Phys. Rev. B 94, 045307 (2016)


Surface or interstitial H is a well known dopant in semiconductors.  
Among tons of papers (I'm ashamed to cite mine :-)) I can suggest  
the classical Van de Walle Nature paper on universal alignment of H  
(Nature 423, 626, 2003)


HTH
Giuseppe

Quoting Matthieu Fortin-Deschênes :


Thanks Giuseppe,

I actually want to passivate the bottom of Si and Ge surfaces, as  
well as one edge of a 2D nanoribbon (antimonene).
I believe fractional charge H atoms would not be useful for these  
kinds of materials. Right?


I was not aware of this strong dopant effect, but I'd be interested  
in reading more about it if you have any reference to suggest.


Thank you,

Matthieu

Giuseppe Mattioli  a écrit :


Dear Matthieu
I don't know which surface you want to passivate, but remember  
that H can also have a strong dopant effect on surfaces (e.g., a  
large upward shift of both band edges, which has been measured on  
C-diamond). Therefore, I used to passivate the unreconstructed end  
of III-V slabs with *pseudo* H atoms, having fractional charge  
which simulate a bulk environment surrounding the bottom layer of  
the slab. They used to be in the online library but they are not  
anymore (maybe for good reasons which I don't know). If you want  
to try I can send you the UPF files. They are NC VBC  
pseudopotentials which should not require more than ecutwfc=40:  
after all you are not interested in structural rearrangement but  
you only need electronic passivation of surface states.

HTH
Giuseppe

Quoting Matthieu Fortin-Deschênes :


Hi all,

I want to use hydrogen to passivate the bottom surface of a  
surface slab. However, I notice that H PPs usually require a high  
ecutwfc, which restricts the size of the system I can consider.


Are there any PPs with lower required ecutwfc available for that purpose?
And would this negatively effect the accuracy of the calculations  
on the other side of the surface slab?


Thank you,

Matthieu Fortin-Deschênes
Polytechnique Montréal

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Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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Re: [QE-users] Soft Hydrogen Pseudopotentials

[Matthieu Fortin-Deschênes]

Thanks Giuseppe,

I actually want to passivate the bottom of Si and Ge surfaces, as well  
as one edge of a 2D nanoribbon (antimonene).
I believe fractional charge H atoms would not be useful for these  
kinds of materials. Right?


I was not aware of this strong dopant effect, but I'd be interested in  
reading more about it if you have any reference to suggest.


Thank you,

Matthieu

Giuseppe Mattioli  a écrit :


Dear Matthieu
I don't know which surface you want to passivate, but remember that  
H can also have a strong dopant effect on surfaces (e.g., a large  
upward shift of both band edges, which has been measured on  
C-diamond). Therefore, I used to passivate the unreconstructed end  
of III-V slabs with *pseudo* H atoms, having fractional charge which  
simulate a bulk environment surrounding the bottom layer of the  
slab. They used to be in the online library but they are not anymore  
(maybe for good reasons which I don't know). If you want to try I  
can send you the UPF files. They are NC VBC pseudopotentials which  
should not require more than ecutwfc=40: after all you are not  
interested in structural rearrangement but you only need electronic  
passivation of surface states.

HTH
Giuseppe

Quoting Matthieu Fortin-Deschênes :


Hi all,

I want to use hydrogen to passivate the bottom surface of a surface  
slab. However, I notice that H PPs usually require a high ecutwfc,  
which restricts the size of the system I can consider.


Are there any PPs with lower required ecutwfc available for that purpose?
And would this negatively effect the accuracy of the calculations  
on the other side of the surface slab?


Thank you,

Matthieu Fortin-Deschênes
Polytechnique Montréal

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I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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[QE-users] Soft Hydrogen Pseudopotentials

[Matthieu Fortin-Deschênes]

Hi all,

I want to use hydrogen to passivate the bottom surface of a surface  
slab. However, I notice that H PPs usually require a high ecutwfc,  
which restricts the size of the system I can consider.


Are there any PPs with lower required ecutwfc available for that purpose?
And would this negatively effect the accuracy of the calculations on  
the other side of the surface slab?


Thank you,

Matthieu Fortin-Deschênes
Polytechnique Montréal

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Re: [Pw_forum] phosphorene monolayer

[Matthieu Fortin-Deschênes]

What values of lattice parameters and band gap did you get? With LDA  
you expect some differences compared to experimental values.

Matthieu

Gautam Gaddemane  a écrit :

> Dear All,
>
> I am trying to calculate the bands tructure for monolayer phosphorene and I
> am just a week old in using quantum espresso.
>> From the bulk unit cell I prepared an input file to relax the structure but
> I was not able to get a good lattice constant nor a good band gap. It would
> be very helpful if someone would guide me in this procedure.
> I have attahced the file I used to relax in this email
>
>
> 
>   calculation='vc-relax',
>   outdir='./',
>   prefix='calc',
>   pseudo_dir='./',
>   verbosity='high',
> /
>
> 
>   ibrav=0,
>   celldm(1)= 8.276999830d0
>   nat=4,
>   ntyp=1,
>   ecutwfc=60,
>   ecutrho=360,
>   input_dft='lda',
>   occupations='smearing',
>   smearing='mv',
>   degauss=0.005d0,
> /
>
> 
>   conv_thr=1d-06,
>   mixing_beta=0.7d0,
> /
> 
>   ion_dynamics='bfgs'
> /
>
> 
>   cell_dynamics='bfgs'
>   cell_dofree='2Dshape'
> /
> ATOMIC_SPECIES
>   P 30.973800d0 P.pw-mt_fhi.UPF
>
> ATOMIC_POSITIONS {crystal}
>
>  P  0.09004 0.0 0.050195117
>  P  0.90967 0.0 0.949804902
>  P  0.59033 0.5 0.949804902
>  P  0.40996 0.5 0.050195117
>
> K_POINTS {automatic}
>
>   12 12 1 0 0 0
>
> CELL_PARAMETERS {alat}
>
>  1.0.0.
>  0.0.7511415530000.
>  0.0.   4.680365292
>
>
> thank you
> Gautam
>
> GAUTAM GADDEMANE
> DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
> UNIVERSITY OF TEXAS AT DALLAS



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Re: [Pw_forum] Applying vdW to only part of a system

[Matthieu Fortin-Deschênes]

You might want to look at this:

https://www.mail-archive.com/pw_forum@pwscf.org/msg28550.html

Matthieu

Ian Shuttleworth  a écrit :

> Hi all
>
> First, thanks for all the replies.
>
> My thoughts are that I want vdW for the adsorbate-adsorbate interaction,
> the adsorbate-substrate interaction but not for the bulk
> substrate-substrate interaction.
>
> When setting up a surface simulation, you can first determine a bulk
> lattice constant. Then, using this lattice constant, you define a slab
> which is the truncated bulk and relax the surface layers and add the
> adsorbates. So, for a material whose bulk lattice constant is reasonably
> well described by non-vdW (e.g. PBEsol) you then overbind if you add vdW
> to bulk component of the simulation, and contract the surface lattice
> constant as a result.
>
> I've found that if I get a +1 to +2% bulk lattice parameter overestimation
> with PBE, I get an equivalent underestimation if I 'turn on' the vdW
> correction. I haven't looked at any other parameters such as formation
> energies yet, as I was interested to get some feedback about this lattice
> constant problem first,
>
> Does this sound reasonable? Or am I thinking about the problem incorrectly?
>
> Again, very kindest thanks for the responses,
>
> Ian
>
>
>
>
>
> Hi Ian, It is possible with dispersion corrections based on the asymptotic
> formula (like XDM or D2, as described by Evren). Why would you want to do
> that, though? In general, dispersion improves the description of metals and
> ionic solids and, one would guess, surfaces. There was a recent paper by
> Perdew and Ruzsinszky on the topic, if memory serves. And I also know for a
> fact that, for instance, B86bPBE-XDM reproduces alkali halide and alkaline
> earth oxide cubic cell lengths with errors of 0.1 angstrom of less once
> vibrational effects are taken into account.
>
> Best,
>
> Alberto
>
> --
> Dr. Alberto Otero de la Roza
> Department of Chemistry,
> University of British Columbia, Okanagan
> Kelowna, British Columbia, Canada V1V 1V7
>
> * Ian Shuttleworth  [2017-09-11 16:33:30 +0100]:
>> Is it possible to apply vdW forces to only a part of system?
>>
>> I am thinking of examples where, for example, a vdW adlayer (e.g. benzene)
>> sits on a surface, and surface doesn't need vdW corrections.
>>
>> If I add the vdw_corr toggle (or if I set an appropriate value
>> to 'input_dft') I've understood that vdW are applied to the entire system -
>> if this is right, how could I make this option more selective?
>>
>> With thanks
>>
>> Ian
>
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Re: [Pw_forum] Require help in vc-relaxing of pure antimony

[Matthieu Fortin-Deschênes]

What phase of antimony do you want to calculate?
If it is rhombohedral gray antimony, there is 6 atoms per unit cell.

Matthieu

stefano de gironcoli  a écrit :

> ecutwfc=50 ecutrho=1000 seriously ?
> if ibrav=4 then celldm2 and celldm4 are not used... and luckily  
> because celldm4 is the cosine of an angle NOT an angle in degrees
> what is not converging is the first scf calculation not the vc-relaxation.
> check your input.. possibly atoms are too close or you are computing  
> too few bands.
> or some other silly error.
> stefano
>
>
> On 16/08/2017 13:47, sayan chaudhuri wrote:
>> Dear QE Experts,
>>
>>  I am running a variable cell relax code for pure Antimony. But  
>> even after 500 iteration the code is not converging. It will be  
>> very helpful if you kindly suggest something regarding the issue.
>> I am attaching my input and output file herewith.
>>
>> Thanking you,
>> Sayan Chaudhuri
>> Research Scholar
>> IIT Indore
>>
>>
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Re: [Pw_forum] Help me to solve a problem in Charge Density Difference calculation using Quantum Espresso

[Matthieu Fortin-Deschênes]

I'm no expert, but I think you need to make the scf calculations with  
the same parameters, especially ecutrho and CELL_PARAMETERS.

Matthieu

Bibhas Manna  a écrit :

> Dear Sir,
>
> Thanking you for your quick reply.
>
> I have used the same parameter for three charges. Following are the input
> pp.x files:
>
>
> *For Substrate + molecules:*
> prefix  = 'PG_4_HCHO_PBE'
> outdir = './tmp/'
> filplot = 'PG_4_HCHO_charge'
> plot_num= 0
>  /
>  
> nfile = 1
> filepp(1) = 'PG_4_HCHO_charge'
> weight(1) = 1.0
> iflag = 2
> output_format = 3
> fileout = 'PG4_HCHO.rho.dat'
> e1(1) =1.0, e1(2)=0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> nx=56, ny=40
>  /
>
> *For Substrate only:*
> prefix  = 'PG_4_PBE'
> outdir = './tmp/'
> filplot = 'PG_4_charge'
> plot_num= 0
>  /
>  
> nfile = 1
> filepp(1) = 'PG_4_charge'
> weight(1) = 1.0
> iflag = 2
> output_format = 3
> fileout = 'PG4.rho.dat'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> nx=56, ny=40,
>  /
>
>
> *For Gas molecule only:*
> prefix  = 'HCHO_PBE'
> outdir = './tmp/'
> filplot = 'HCHO_charge'
> plot_num= 0
>  /
>  
> nfile = 1
> filepp(1) = 'HCHO_charge'
> weight(1) = 1.0
> iflag = 2
> output_format = 3
> fileout = 'HCHO.rho.dat'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
>  nx=56, ny=40,
> /
>  I am actually getting  error in the reading of the filepp(2) as follows:
>
> Reading header from file  PG_4_HCHO_charge
>
>Info: using nr1, nr2, nr3 values from input
>  Reading data from file  PG_4_HCHO_charge
>  Reading data from file  PG_4_charge
>
>   
> %%
>  Error in routine chdens (1):
>  incompatible gcutm or dual or ecut
>   
> %%
>
>  stopping ...
>
> Thanks.
> Bibhas
>
> On Sat, Aug 12, 2017 at 7:59 PM, stefano de gironcoli 
> wrote:
>
>> you need to compute the three charges with the same parameters
>>
>> stefano
>>
>>
>> On 12/08/2017 16:20, Bibhas Manna wrote:
>>
>> Dear All,
>>
>> I am very new to Quantum Espresso. I want to get a charge density
>> difference plot for a gas molecule adsorbed on the single layer graphene
>> surface. Presently I am using pp.x to compute the same in QE v.5.1
>> following an equation:
>>
>> ∆ρ=ρAB – ρA-ρB
>>
>> Where, ρAB, ρA and ρB are the charge densities of graphene -molecule
>> complex, graphene and molecule respectively. I have successfully computed
>> all of these three charge densities using pp.x. Now, I am trying to find
>> out the charge density difference using pp.x with nfile = 3, while all of
>> these three charge files are available to me as inputs.
>>
>> Unfortunately, I got an error in the output log:
>> *Error in routine chdens (1):
>>incompatible gcutm or dual or ecut*
>>
>> Since, I have different number of atoms in each of the three files, how
>> can I make the charge files having same number of atomic coordinates?
>>
>> I am sharing my input and output files for your kind considerations.
>>
>> Can you help me to solve this problem?
>>
>> Thanks with regards,
>> Bibhas Manna
>> Research Scholar,
>> IIT Kharagpur, India
>>
>>
>>
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>>
>>
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Re: [Pw_forum] Cell Relaxation

[Matthieu Fortin-Deschênes]

Dear Ali,

First, if you want to relax the cell, you need to use calculation='vc-relax'
Then you need to specify the namelist , and also your namelist  
 is empty. As for what to put in those, you can look at the input  
file description:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm5993056
There are also examples on how to do this.

For your second question, the functional used is taken from the  
pseudopotential file and is specified in the file name of the  
pseudopotential. In your case you have pbe (gga). You can just change  
the pseudopotential to have another functional. I don't know anything  
about phonon calculations so I can't tell you what is more accurate.

What you get in the output file is cell parameters in alat units. That  
is in units of celldm(1). I don't think you can change it, but it only  
takes a few seconds to convert by yourself.

Also you should use a Gamma centered k-points mesh for hexagonal  
lattices and (6x6x1) seems too low to me. Did you check convergence  
wrt number of kpoints?

Matthieu Fortin-Deschênes
Polytechnique Montréal



ali.kamran...@yahoo.com a écrit :

> Dear users,
> First, I want to apologize for my very basic question. I am new to DFT.
> I know first step to do any kind of DFT calculations is to relax the  
> cell parameters. But unfortunately, I don't know how to do that. I  
> tried to run the attached input file but it does not seem to be  
> correct.
> My second question is what will differ if I want to relax my  
> structure using LDA or GGA? Is it just using  
> different pseudopotential files? Which approximation is more  
> accurate for phonon calculations?
> And my last question is, is it possible to obtain the relaxed cell  
> parameters based on angstrom?
> Thank you so much in advance.
> Kind Regards,
> Ali



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[Pw_forum] Projwfc.x for fatbands

[Matthieu Fortin-Deschênes]

Dear all,

I'm trying to understand the process of calculating fatbands like in  
PP/examples/example05.

Here is my problem:

When I use lsym=.TRUE. in the input of bands.x, I get the output file  
with 3 columns similar to feo_af.bands.all with the kpoints, energies  
and weights. However, some of the band crossings seem wrong.


When I use lsym=.FALSE. in the input of bands.x, the band crossing  
problem is solved (at least partially), but i dont get the weighted 3  
column output file of the bandstructure.

My question is:

Is there a physical reason why the weighted bands cannot be obtained  
when lsym=.TRUE. is used in the input of bands.x, or is it just not  
implemented?

Thank you

Matthieu Fortin-Deschênes
Polytechnique Montréal


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Re: [Pw_forum] optB86b-vdW pseudopotential

[Matthieu Fortin-Deschênes]

Thanks for the reply.

So just to be clear, i should:

1)Generate a pseudopotential using the optB86b functional
2)Generate the vdw_kernel_table
3)Specify vdw-df-ob86 in input_dft

Is that correct?

Thanks again

Aldo Ugolotti  a écrit :

> You also have to run, just for the first time, the command:
> generate_vdW_kernel_table.x
> that will create the database of input functionals and i guess that you
> have to copy the database in your local pseudopotential files directory
>
> Good luck,
>
> Aldo Ugolotti
> Università degli Studi di Milano-Bicocca
>
>> you should use "input_dft="vdw-df-ob86".
>> (see QE/Modules/funct.f90)
>>
>> ?2016-07-27 03:54:41,plgong???
>> Hi all,
>>
>> I want to make calculations using optB86b-vdW functional. If I
>> understand correctly, I just need to specify 'vdw-DF' in input_DFT and
>> use a pseudopotentials generated with the optB86b functional?
>>
>> If so, is there an available database for optB86b pseudopotentials? I
>> wasn't able to find one.
>> Otherwise, could you suggest me any good references explaining the
>> basics of pseudopotentials and pseudopotential generation?
>>
>> Thank you very much
>>
>>
>> Matthieu Fortin-Desch?nes
>> Polytechnique Montr?al



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[Pw_forum] optB86b-vdW pseudopotential

[Matthieu Fortin-Deschênes]

Hi all,

I want to make calculations using optB86b-vdW functional. If I
understand correctly, I just need to specify 'vdw-DF' in input_DFT and
use a pseudopotentials generated with the optB86b functional?

If so, is there an available database for optB86b pseudopotentials? I
wasn't able to find one.
Otherwise, could you suggest me any good references explaining the
basics of pseudopotentials and pseudopotential generation?

Thank you very much


Matthieu Fortin-Deschênes
Polytechnique Montréal


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[Pw_forum] optB86b-vdW

[Matthieu Fortin-Deschênes]

Hi all,

I want to make calculations using optB86b-vdW functional. If I  
understand correctly, I just need to specify 'vdw-DF' in input_DFT and  
use a pseudopotentials generated with the optB86b functional?

If so, is there an available database for optB86b pseudopotentials? I  
wasn't able to find one.
Otherwise, could you suggest me any good references explaining the  
basics of pseudopotentials and pseudopotential generation?

Thank you very much


Matthieu Fortin-Deschênes
Polytechnique Montréal


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Re: [Pw_forum] Grimme C_ij for epitaxial graphene

[Matthieu Fortin-Deschênes]

Paolo and Martin,

Thanks a lot for the advice, I am now looking at the details of how to do it.

Martin,

They are metal substrates. I will look at those papers in details. I  
was planning to use both Grimme corrections and a VdW functional to  
compare the results. Thanks again for the advice. Very helpful.

Matthieu

Martin Andersson <m...@nano.ku.dk> a écrit :

> Hi Matthieu,
>
>   I was curious as to which substrates you are putting graphene 
> on.  
> Because if you are looking at either ionic solids or metals, the  
> Grimme corrections are going to be a bit too strong, but it can be  
> fixed. We have had success for calculating adsorption energies on  
> minerals by reducing the C6 parameter for the cations in the  
> substrate by about an order of magnitude (we decreased the parameter  
> by 33 for Ca in calcite in (Okhrimenko et al Langmuir 29,  
> 11062-11073,(2013)). The idea came from Ehrlich et al ChemPhysChem  
> 12, 3414-3420,(2011). For cations in ionic solids (e.g. oxides,  
> minerals), the polarisability is significantly smaller  because of  
> the smaller electron cloud of a cation compared to the corresponding  
> neutral atom.
>
>   For metals, I had good success in Andersson MP Journal of  
> Theoretical Chemistry 2013, Article ID 327839,(2013), where I  
> modified Grimme corrections to make it work better for metals by  
> using a shorter cutoff to simulate screening by the conduction  
> electrons and switching the C6 parameters for the metal to the  
> parameter of the noble gas in the row above.
>
>   In either of the two cases, you only need to modify the  
> mm_dispersion.f90 file and recompile. I have a couple of different  
> mm_dispersion.f90 files lying around if you need one...
>
>   Or you could of course also switch to a suitable vdw functional 
> if  
> you like instead.
>
>   Cheers and good luck,
>
> 
> Martin P. Andersson
> Associate Professor
> Nano-Science Center, Department of Chemistry
> University of Copenhagen, Denmark
>
> Tel: +45 3532 0280
> Mobile: +46 733 893091
> E-mail: m...@nano.ku.dk
> 
>
>
>
>
>
>
>
>
>
>> On 12 May 2016, at 20:22, Matthieu Fortin-Deschênes  
>> <matthieu.fortin-desche...@polymtl.ca> wrote:
>>
>> Hi all,
>>
>> I'm trying to calculate some basic properties of graphene on various
>> substrates using Grimme correction for VdW interactions. The Grimme
>> corrections seem to deteriorate the results (lattice parameter and
>> binding energy) of the graphene as well of the substrate compared to
>> experimental results.
>>
>> I was wondering if it's possible to set C_ij=0 for i=j (no correction
>> for C-C interactions, as well as substrate-substrate interaction), but
>> non-zero C_ij for graphene-substrate interactions. As far as i know,
>> C_i are defined for each element and C_ij is calculated from
>> sqrt(C_i*C_j). I would like to set all C_ij by myself.
>>
>> Thank you
>>
>> Matthieu Fortin-Deschênes
>> Polytechnique Montreal
>>
>>
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[Pw_forum] Grimme C_ij for epitaxial graphene

[Matthieu Fortin-Deschênes]

Hi all,

I'm trying to calculate some basic properties of graphene on various  
substrates using Grimme correction for VdW interactions. The Grimme  
corrections seem to deteriorate the results (lattice parameter and  
binding energy) of the graphene as well of the substrate compared to  
experimental results.

I was wondering if it's possible to set C_ij=0 for i=j (no correction  
for C-C interactions, as well as substrate-substrate interaction), but  
non-zero C_ij for graphene-substrate interactions. As far as i know,  
C_i are defined for each element and C_ij is calculated from  
sqrt(C_i*C_j). I would like to set all C_ij by myself.

Thank you

Matthieu Fortin-Deschênes
Polytechnique Montreal


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