[Pw_forum] cutoff convergence of sapphire for elastic properties
Am Mon, 7 May 2012 14:22:58 -0400 schrieb Mike Mehl : > To follow up on Nicola's point, the bulk modulus of sapphire is 240 > GPa or 2400 kbar > (http://www.mt-berlin.com/frames_cryst/descriptions/sapphire.htm). So > a 1 kbar error corresponds to a very small change in volume. > > If we use the quick and dirty Birch equation of state: > > P(V) = 3/2 K0 [ (V0/V)^(7/3) - (V0/V)^(5/3)] > > with K0 = 2400 kbar and ask what volume will produce a 1 kbar change > in pressure we get > > delta V/V0 = +/- 0.0004 > > Considering the normal errors in DFT, it's not worth trying to > converge the stress to the 1 kbar accuracy you're trying to achieve. But to get the elastic constants in the elastic regime, i would like then apply strains of serveral per mill, which is of the same order of magnitude, i.e. also corresponds to changes of the stress tensor of the order of 1 kbar, which means that errors in the kbar range would be too high. An alternative could be the calculation of the elastic constants using the second derivative of the energy. But this won't work for big supercells due to the computation time and the number of measuring points needed. > > On Mon, May 7, 2012 at 10:07 AM, Nicola > Marzari wrote: > > > > > How much does 1 kbar error translates into an error in lattice > > parameter? (keep atoms fixed, using relative coordinates, cutoff > > fixed, and expand celldm(1) by 0.3% - what's the change in stress? > > that change should be very well converged) > > > > -- > Michael Mehl > US Naval Research Laboratory > Washington DC > (Home email)
[Pw_forum] cutoff convergence of sapphire for elastic properties
that was also done. JB Am Mon, 7 May 2012 09:41:35 -0400 schrieb Iyad AL-QASIR : > Hello, > Try first to relax the atomic positions, then relax the structure. > > Thanks > > > On Mon, May 7, 2012 at 9:22 AM, J?rg Buchwald > > wrote: > > > Hi, > > i tested a relaxed sapphire structure using a 10x10x10 k point set > > with a cutoff energy up to 250 Ry. Even at this Energy, a change of > > +/- 5 Ry in the cutoff lead to stresses of the order of 1 kbar. > > I used for Al and O pbe-n-van US pseudo potentials from the pseudo > > folder of quantum espresso. But also pbe-sp-van for Al and rrkjus > > for oxygen led to the same problem. > > I don't have a clue how high the cutoff must be, but 250 Ry seems > > to be far too high. Is that a problem of the pseudopotentials or > > does it have something to do with physical structure of sapphire? > > Thx for any hints, > > J?rg Buchwald > > > > -- > > Leibniz-Institut fuer Oberflaechenmodifizierung e.V. > > > > Permoserstrasse 15 > > 04318 Leipzig > > GERMANY > > > > Phone: +49 341 / 235-3367 > > Web: http://www.uni-leipzig.de/~agmayr > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr
[Pw_forum] cutoff convergence of sapphire for elastic properties
Hi, i tested a relaxed sapphire structure using a 10x10x10 k point set with a cutoff energy up to 250 Ry. Even at this Energy, a change of +/- 5 Ry in the cutoff lead to stresses of the order of 1 kbar. I used for Al and O pbe-n-van US pseudo potentials from the pseudo folder of quantum espresso. But also pbe-sp-van for Al and rrkjus for oxygen led to the same problem. I don't have a clue how high the cutoff must be, but 250 Ry seems to be far too high. Is that a problem of the pseudopotentials or does it have something to do with physical structure of sapphire? Thx for any hints, J?rg Buchwald -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr
[Pw_forum] Al pseudopotential and elastic properties
Hi, does anyone has any experiences with the Al pseudopotentials and the elastic constants? I was testing Al.pbe-n-van.UPF with which I could reproduce the elastic constant and the cohesive energy quite well, but using the output of the stress matrix I get a way too high results for C11(>150GPa) at a strain of 0.001. Appliying strains about >3%, I get results which are quite relastic for C11(90-110 GPa). I thought that this has something to do whith the kind of approximation, so I also created a ultrasoft (PZ-)LDA potential with the vanderbilt code and tried the normconserving Al.pz-vbc.UPF, which gave me similar results. I applied the strain by stretching the cell vectors and performing a 'relax'-simulation. This is my input file for a rel. strain of 0.003: --- calculation='relax' prefix='Al-test11', pseudo_dir='/home/jbuchw/espresso-4.3.2/pseudo' outdir = '/home/jbuchw/scratch', tstress=.true. disk_io='none' etot_conv_thr=1.0D-10 forc_conv_thr=1.0D-10 / ibrav= 0, celldm(1) =7.6271186 nat= 4, ntyp= 1, ecutwfc = 85.0 occupations='smearing' smearing='mp' degauss=0.0007 / diagonalization='david' mixing_mode='plain' conv_thr=1.0D-10 / bfgs_ndim=3 / ! cell_dofree='yz' / ATOMIC_SPECIES Al 26.981539 Al.pbe-n-van.UPF ATOMIC_POSITIONS crystal Al 0.00 0.00 0.00 Al 0.50 0.50 0.00 Al 0.00 0.50 0.50 Al 0.50 0.00 0.50 K_POINTS automatic 14 14 14 0 0 0 CELL_PARAMETERS 0.9995541042 0.0 0.0 0.0 0.996564411 0.0 0.0 0.0 0.996564411 -- Am I doing something wrong, or does it have something to do with the pseudopotential? Regards, J?rg PS: I also tried to get C11 by the second derivative the Energy fitting quadratic function which gave me C11=75.6GPa but this would assume that the elastic constant is constant over the strain range(which could be showed that's not the case for small strains(<0.01) using the numerical second derivative). -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr
[Pw_forum] conflicting values icorr /igcx
Am Tue, 1 Nov 2011 22:04:42 +0100 schrieb Paolo Giannozzi : > > On Nov 1, 2011, at 20:19 , joerg.buchwald at iom-leipzig.de wrote: > > > I'm using QE 4.3.2 and as pseudopotentials, i tried nearly all ncpp > > which are in the pseudo package from the QE site: e.g. Al.pbe- > > rrkj.UPF, > > Al.pz-vbc.UPF, O.blyp-mt.UPF, O.pz-mt.UPF. > > if you use PP generated with different XC, you need to specify which > XC you want with input variable "input_dft". It works for me (see > attached) Thanks, that's actually logical. cheers, j?rg
[Pw_forum] conflicting values icorr /igcx
Hi, I'm trying to model bulk sapphire with norm conserving potentials for O respectively for Al and O and I get the following error: -- stopping ... from set_dft_from_name : error # 1 conflicting values for icorr -- The same input file worked with ultrasoft and gradient corrected ultrasoft potentials, but with any of the ncpp (which I got also from the quantum espresso website) it didn't. I can't figure out what the sourcecode really does at that point and the error seems to be quite undocumented. Thanks for hints, J?rg -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY Phone: +49 341 / 235-3367 Web: http://www.uni-leipzig.de/~agmayr
[Pw_forum] QE v4.3.2 failed to read the input file of v4.3
Thanks, that was it. I found a forbidden linebreak in input_tmp.in So as mentioned before it was a problem caused by the character length... Regards, J?rg Buchwald -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY
[Pw_forum] QE v4.3.2 failed to read the input file of v4.3
thats strange. here is the output file, it is the same error message, as the one of longhua. -- Program PWSCF v.4.3.2 starts on 16Aug2011 at 15:59: 5 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 8 processors R & G space division: proc/pool =8 Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 4 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Reading input from stdin %% from read_namelists : error #17 %% from read_namelists : error #17 reading namelist system %% %% from read_namelists : error #17 reading namelist system %% reading namelist system %% stopping ... %% from read_namelists : error #17 reading namelist system %% %% from read_namelists : error #17 reading namelist system %% stopping ... %% from read_namelists : error #17 reading namelist system %% stopping ... %% from read_namelists : error #17 reading namelist system %% stopping ... stopping ... stopping ... stopping ... %% from read_namelists : error #17 reading namelist system %% stopping ... -- thx, J?rg J?rg Buchwald Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY
[Pw_forum] QE v4.3.2 failed to read the input file of v4.3
Hi, i have the same problem (with the same error message) with v4.3.2, with v4.3.1 it works fine. here my input file: -- calculation='vc-relax' prefix='silicon-vanderbilt', pseudo_dir='/home/joerg/espresso-4.3.1/pseudo' outdir = '/home/joerg/scratch', tstress=.true. disk_io='none' / ibrav= 8, celldm(1) =10.33425, celldm(2)=1.0, celldm(3)=10.00, nat= 80, ntyp= 1, ecutwfc = 55.0 / diagonalization='david' mixing_mode='plain' / / / ATOMIC_SPECIES Si 28.086 Si.pbe-n-van.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 Si 0.50 0.50 0.00 Si 0.75 0.75 0.25 Si 0.50 0.00 0.50 Si 0.75 0.25 0.75 Si 0.00 0.50 0.50 Si 0.25 0.75 0.75 Si 0.00 0.00 1.00 Si 0.25 0.25 1.25 Si 0.50 0.50 1.00 Si 0.75 0.75 1.25 Si 0.50 0.00 1.50 Si 0.75 0.25 1.75 Si 0.00 0.50 1.50 Si 0.25 0.75 1.75 Si 0.00 0.00 2.00 Si 0.25 0.25 2.25 Si 0.50 0.50 2.00 Si 0.75 0.75 2.25 Si 0.50 0.00 2.50 Si 0.75 0.25 2.75 Si 0.00 0.50 2.50 Si 0.25 0.75 2.75 Si 0.00 0.00 3.00 Si 0.25 0.25 3.25 Si 0.50 0.50 3.00 Si 0.75 0.75 3.25 Si 0.50 0.00 3.50 Si 0.75 0.25 3.75 Si 0.00 0.50 3.50 Si 0.25 0.75 3.75 Si 0.00 0.00 4.0 Si 0.25 0.25 4.25 Si 0.50 0.50 4.00 Si 0.75 0.75 4.25 Si 0.50 0.00 4.50 Si 0.75 0.25 4.75 Si 0.00 0.50 4.50 Si 0.25 0.75 4.75 Si 0.00 0.00 5.0 Si 0.25 0.25 5.25 Si 0.50 0.50 5.00 Si 0.75 0.75 5.25 Si 0.50 0.00 5.50 Si 0.75 0.25 5.75 Si 0.00 0.50 5.50 Si 0.25 0.75 5.75 Si 0.00 0.00 6.0 Si 0.25 0.25 6.25 Si 0.50 0.50 6.00 Si 0.75 0.75 6.25 Si 0.50 0.00 6.50 Si 0.75 0.25 6.75 Si 0.00 0.50 6.50 Si 0.25 0.75 6.75 Si 0.00 0.00 7.0 Si 0.25 0.25 7.25 Si 0.50 0.50 7.00 Si 0.75 0.75 7.25 Si 0.50 0.00 7.50 Si 0.75 0.25 7.75 Si 0.00 0.50 7.50 Si 0.25 0.75 7.75 Si 0.00 0.00 8.0 Si 0.25 0.25 8.25 Si 0.50 0.50 8.00 Si 0.75 0.75 8.25 Si 0.50 0.00 8.50 Si 0.75 0.25 8.75 Si 0.00 0.50 8.50 Si 0.25 0.75 8.75 Si 0.00 0.00 9.0 Si 0.25 0.25 9.25 Si 0.50 0.50 9.00 Si 0.75 0.75 9.25 Si 0.50 0.00 9.50 Si 0.75 0.25 9.75 Si 0.00 0.50 9.50 Si 0.25 0.75 9.75 K_POINTS automatic 7 7 7 0 0 0 --- Best, J?rg Buchwald -- J?rg Buchwald Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY
[Pw_forum] strange error with monoclinic structure
Am Fri, 29 Jul 2011 08:09:59 +0200 schrieb Paolo Giannozzi : > > On Jul 28, 2011, at 17:04 , J?rg Buchwald wrote: > > > from davcio : error #99 > > error while reading from file > > if this happens at the beginning of the calculation, there may > be corrupted or inconsistent restart file in the scratch directory. > Your input works fine for me : >http://www.fisica.uniud.it/~giannozz/public/boh.out > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 ok sorry for that question, i thought the state is saved by the identifier prefix only, and mainly because of the disk_io switch turned off, i didn't thought that it would have any influence... Thx, J?rg -- J?rg Buchwald Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY
[Pw_forum] strange error with monoclinic structure
Hi, to get the shear modulus i performed some simulations with a monoclinic silicon lattice. I simulated with different angles. For celldm(4)=0.004 or celldm(4)=0.002 it works, but if i set celldm(4)=0.003 i get the following error -- %% from davcio : error #99 error while reading from file %% stopping ... %% from davcio : error #99 error while reading from file %% stopping ... -- an here is my input file: -- calculation='scf' prefix='silicon', pseudo_dir='/home/joerg/espresso-4.3.1/pseudo' outdir = '/home/joerg/scratch', tstress=.true. disk_io='none' / ibrav= 12, celldm(1) =10.334309, celldm(2)=1.0, celldm(3)=1.00, celldm(4)=0.003, nat= 8, ntyp= 1, ecutwfc = 50.0,ecutrho=500.0 / diagonalization='cg' mixing_mode='plain' / / / ATOMIC_SPECIES Si 28.086 Si.pbe-n-van.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 Si 0.50 0.50 0.00 Si 0.75 0.75 0.25 Si 0.50 0.00 0.50 Si 0.75 0.25 0.75 Si 0.00 0.50 0.50 Si 0.25 0.75 0.75 K_POINTS automatic 15 15 15 0 0 0 -- Do you have any idea what the problem could be? Thx, J?rg -- J?rg Buchwald Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY
[Pw_forum] problem in calculating the binding energies with pwscf
Hi,
Thx, now it looks much better. I set the starting_magnetization to 10
only for test reasons, but as you said, it was the wrong switch.
Regards,
J?rg
--
Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY
Am Thu, 21 Jul 2011 11:13:43 -0400 (EDT)
schrieb elbuesta at icqmail.com:
> Hello Joerg Buchwald,
>
> a few comments. Starting magnetization should be between -1 and 1. 1
> means that all available electrons from the PP have spin up. Also, if
> you want to do spin unrestricted calculations, you should set
> nspin=2. Only starting magnetization does not do anything.
>
> In addition, I wouldn't compare the energy of the bulk and the
> isolated atom this way because the cutoff on the WFC is quite
> different for each case: energy differences converge much faster than
> the total energy. But I don't think that is the problem here, only
> the magnetization is.
>
> I slightly modified your inputs and got 4.5eV. If I remember well,
> this value is okay. I hope it helps. All best!
>
> Free Si atom:
>
>
> prefix='si_free',
> pseudo_dir='/home/alex/pseudo'
> outdir = '/scratch/alex',
> /
>
> ibrav= 1, celldm(1) =25, nat= 1, ntyp= 1,
> ecutwfc =
> 30.0,occupations='fixed',nspin=2,tot_magnetization=2.,nosym=.true., /
>
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
> Si 0.50 0.50 0.50
> K_POINTS gamma
> ..
>
> Bulk Si:
>
>
> prefix='silicon',
> pseudo_dir='/home/alex/pseudo'
> outdir = '/scratch/alex',
> /
>
> ibrav= 2, celldm(1) =10.263142, nat= 2, ntyp= 1,
> ecutwfc = 40.0,
> /
>
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
> Si 0.00 0.00 0.00
> Si 0.25 0.25 0.25
> K_POINTS automatic
> 9 9 9 1 1 1
>
>
>
>
> -Original Message-
>
> From: J?rg Buchwald
> To: pw_forum
> Sent: Thu, Jul 21, 2011 3:15 pm
> Subject: [Pw_forum] problem in calculating the binding energies with
> pwscf
>
>
> Hello,
> I'm performing some first test-calculations with pwscf, where I try to
> get the binding energy of bulk silicon. The problem is, that the
> resulting energy, which should be the difference of the total
> energy of silicon crystal structure and the a free atom, is about 3eV
> too low. I used different pseudopotentials, different
> lattice-parameters and I also tested the convergencies (with k and
> the energy-cut-off) which worked, but I don't have a clue what a made
> wrong.
>
> Here are my Input files:
>
> ---
>
> prefix='silicon',
> pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
> outdir = '/home/joerg/scratch',
> /
>
> ibrav= 2, celldm(1) =10.263142, nat= 2, ntyp= 1,
> ecutwfc = 30.0,
> /
>
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
> Si 0.00 0.00 0.00
> Si 0.25 0.25 0.25
> K_POINTS automatic
> 9 9 9 1 1 1
> ---
>
> and for the free atom:
>
> ---
>
> prefix='silicon',
> pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
> outdir = '/home/joerg/scratch',
> /
>
> ibrav= 0, celldm(1) =50.2, nat= 1, ntyp= 1,
> ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
> /
>
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pbe-n-van.UPF
> ATOMIC_POSITIONS
> Si 0.50 0.50 0.50
> K_POINTS gamma
>
> CELL_PARAMETERS {cubic}
> 1.00 0.00 0.00
> 0.00 1.00 0.00
> 0.00 0.00 1.00
> ---
>
> It would be nice if someone could help me.
> Thx & regards,
> J?rg Buchwald
>
>
> Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
> Permoserstrasse 15
> 04318 Leipzig
> GERMANY
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
[Pw_forum] problem in calculating the binding energies with pwscf
Hello,
I'm performing some first test-calculations with pwscf, where I try to
get the binding energy of bulk silicon. The problem is, that the
resulting energy, which should be the difference of the total
energy of silicon crystal structure and the a free atom, is about 3eV
too low. I used different pseudopotentials, different
lattice-parameters and I also tested the convergencies (with k and
the energy-cut-off) which worked, but I don't have a clue what a made
wrong.
Here are my Input files:
---
prefix='silicon',
pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
outdir = '/home/joerg/scratch',
/
ibrav= 2, celldm(1) =10.263142, nat= 2, ntyp= 1,
ecutwfc = 30.0,
/
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-n-van.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
K_POINTS automatic
9 9 9 1 1 1
---
and for the free atom:
---
prefix='silicon',
pseudo_dir='/home/joerg/espresso-4.3.1/pseudo'
outdir = '/home/joerg/scratch',
/
ibrav= 0, celldm(1) =50.2, nat= 1, ntyp= 1,
ecutwfc = 80.0,occupations='fixed',starting_magnetization(1)=10,
/
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-n-van.UPF
ATOMIC_POSITIONS
Si 0.50 0.50 0.50
K_POINTS gamma
CELL_PARAMETERS {cubic}
1.00 0.00 0.00
0.00 1.00 0.00
0.00 0.00 1.00
---
It would be nice if someone could help me.
Thx & regards,
J?rg Buchwald
Leibniz-Institut fuer Oberflaechenmodifizierung e.V.
Permoserstrasse 15
04318 Leipzig
GERMANY
