[Pw_forum] pwcond transmission tran_file
Dear Jonathan It is in summary_tran.f90 regards, Alexander 2012/7/10 Jonathan Trinastic > Hi all, > > This question should probably be directed to Alexander Smogunov, as it > is about the pwcond code. I'm currently doing some transport > calculations with FeCo / MgO systems - I'm getting expected results > using a 4 layer MgO, however, I want to compare to larger barrier > widths, but the total transmissions given in the tran_file are small, > and I require more than the seven decimal limit for the minority channel > transmissions results. > > Can you tell me where in the code I can extend the output for the > tran_file so I can see results to greater than seven decimal places? > > Thanks, > Jonathan > > -- > Jonathan Trinastic, M.S. > Graduate Student > Department of Physics > University of Florida > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/7ee9af1a/attachment.htm
[Pw_forum] Error #19 MoS2 ecutoff convergence test
Well, the error actually is very small, please check carefully next time, since
this must only due to your own careless~
in &system, to define the number of band, we use the parameter "nbnd" instead
of "nband"..
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-07-10 17:09:37,"Sohail Ahmad" wrote:
| Dear QE users
I am unable to understand the reason behind error #19
Kindly help
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
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...
%%
from read_namelists : error #19
reading namelist system
%%
stopping ...
---
#!/bin/sh
for i in 30 35 40 45 50 55 60 65
do
#j=$[$i*8]
echo " calculation ecutoff $i is running "
cat >> MoS2$i.in << EOF
&control
calculation = 'scf',
restart_mode = 'from_scratch',
prefix = 'MoS2',
pseudo_dir = '/home/sohail/espresso-4.2.1/pseudo',
outdir = './OUT'
/
&system
ibrav = 4, celldm(1) = 5.9715031, celldm(3) = 3.89, nat = 6, ntyp = 2,
ecutwfc = $i,
ecutrho = 300,
nband = 10,
occupations = 'smearing', smearing = 'gaussian', degauss= 0.001,
nspin = 2,
starting_magnetization(1) = 0.5d0,
/
&electrons
mixing_beta = 0.3,
conv_thr = 1.0d-9,
/
ATOMIC_SPECIES
Mo 95.96 Mo.pbe-paw-nh.UPF
S 32.06 S.pbe-van_bm.UPF
ATOMIC_POSITIONS {crystal}
Mo 0. 0.6667 0.2500
Mo 0.6667 0. 0.7500
S 0. 0.6667 0.6200
S 0.6667 0. 0.1200
S 0.6667 0. -0.6200
S 0. 0.6667 -0.1200
K_POINTS AUTOMATIC
4 4 4 1 1 1
EOF
pw.x < MoS2$i.in> MoS2$i.out
rm -rf OUT/*
done
---
Sohail Ahmad
King Khalid University
Saudi Arabia
|
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[Pw_forum] Calculation of Gibbs free energies
On Tue, Jul 10, 2012 at 4:44 PM, Torstein Fjermestad < torstein.fjermestad at kjemi.uio.no> wrote: > The problem is that I have so far only managed to complete step 1, to > compute the phonons. I am currently doing test calculations on a water > molecule and this is the input file of the phonon calculation: > > ... This calculation crashes presumably because it expects a file called > h2o.dynG0. But from where do I get this file? As far as I can see the > phonon calculation only produces the file h2o.dynG, not a h2o.dynG0 > file. > > Dear Torstein, the problem in your case is that q2r.x expects to find a phonon *dispersion* calculation, i.e. the phonon computed over a regular grid of q-points n reciprocal space. On the other hand, you only computed the phonons at Gamma. It is true that Gamma is just a 1x1x1 grid, and if you are sure it is enough to describe your system you can manage to convince q2r to use it. You need to do the following: 1. move h2o.dynG to h2o.dynG1 2. create a file called h2o.dynG0 which this inside: 1 1 1 1 0.0 0.0 0.0 3. try again with q2r.x Alternatively, you can just repeat the phonon calculation with ldisp = .true.; if you want your grid to be just the Gamma point you specify nq1=1, nq2=1, nq3=1. I stress that a single-point sampling may not be enough to describe accurately the properties of your system (unless the supercell is very large) but this you need to check for yourself. good work -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/fa55df1e/attachment-0001.htm
[Pw_forum] Calculation of Gibbs free energies
On Jul 10, 2012, at 16:44 , Torstein Fjermestad wrote: > this is the input file of the phonon calculation: this is the input file for a SINGLE phonon calculation. You need to specify "disp=.true." and a wave-vector grid to get the phonon dispersions needed to calculate interatomic force constants P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Error #19 MoS2 ecutoff convergence test
Dear QE users
I am unable to understand the reason behind error #19
Kindly help
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
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...
?%%
from? read_namelists? : error #??? 19
? reading namelist system
?%%
stopping ...
---
#!/bin/sh
for i in 30 35 40 45 50 55 60 65
do
#j=$[$i*8]
echo " calculation ecutoff $i is running "
cat >> MoS2$i.in << EOF
?&control
? calculation = 'scf',
? restart_mode = 'from_scratch',
? prefix = 'MoS2',
? pseudo_dir = '/home/sohail/espresso-4.2.1/pseudo',
? outdir = './OUT'
?/
?&system
? ibrav = 4, celldm(1) = 5.9715031, celldm(3) = 3.89, nat = 6, ntyp = 2,
? ecutwfc = $i,
? ecutrho = 300,
? nband = 10,
? occupations = 'smearing', smearing = 'gaussian', degauss= 0.001,
? nspin = 2,
? starting_magnetization(1) = 0.5d0,
?/
?&electrons
? mixing_beta = 0.3,
? conv_thr = 1.0d-9,
?/
ATOMIC_SPECIES
Mo? 95.96? Mo.pbe-paw-nh.UPF
S?? 32.06? S.pbe-van_bm.UPF
ATOMIC_POSITIONS {crystal}
Mo? 0.? 0.6667? 0.2500
Mo? 0.6667? 0.? 0.7500
S?? 0.? 0.6667? 0.6200
S?? 0.6667? 0.? 0.1200
S?? 0.6667? 0. -0.6200
S?? 0.? 0.6667 -0.1200
K_POINTS AUTOMATIC
4 4 4 1 1 1
EOF
pw.x < MoS2$i.in> MoS2$i.out
rm -rf OUT/*
done
---
Sohail Ahmad
King Khalid University
Saudi Arabia
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[Pw_forum] Calculation of Gibbs free energies
Dear all, In one of my projects I would need to compute the Gibbs free energies of structures along a reaction path. After looking through the QE webpage, the pw_forum, and the documentation in the quantum espresso installation directory I think I understand the general procedure: 1. one calculates the phonons 2. one computes the interatomic Force Constants with the q2r.x program 3. one uses the matdyn.x to produce input for the F_QHA.x program 4. with the F_QHA.x program one can compute the Gibbs free energy and other thermodynamical properties. (please correct me if I have misunderstood this general procedure) The problem is that I have so far only managed to complete step 1, to compute the phonons. I am currently doing test calculations on a water molecule and this is the input file of the phonon calculation: phonons of H2O in super cell at Gamma &inputph outdir='./', prefix='h2o', amass(1)=1.01, amass(2)=16.01, fildyn='h2o.dynG', trans= .true. / 0.0 0.0 0.0 I then try to run the q2r.x calculation with the following input: test of q2r calculation &input fildyn='h2o.dynG', flfrc='h2o-output-q2r.fc', zasr='no' This calculation crashes presumably because it expects a file called h2o.dynG0. But from where do I get this file? As far as I can see the phonon calculation only produces the file h2o.dynG, not a h2o.dynG0 file. I am completely lost at the moment so I would appreciate if anyone could help me with carrying out the q2r calculation correctly. Thank you very much in advance, Yours sincerely, Torstein Fjermestad, University of Oslo, Norway
[Pw_forum] segfault in projwfc calculation
On Jul 10, 2012, at 12:46 , Giuseppe Mattioli wrote: > mpirun noticed that process rank 2 with PID 12250 on node compute-1-1 > exited on signal 11 (Segmentation fault). it works for me both in serial and in parallel execution. It is likely a compiler or library problem. There is little that can be done in cases like this P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Old problem with cppp.x
Problem solved! My mistake! I was using the same parallel running script that I use for cp.x to run cppp.x! Just don't run it with mpirun! It's serial! Thanks a lot, Negar On Mon, Jul 9, 2012 at 6:01 PM, Negar Ashari Astani wrote: > Dear Gabriele, > > Thanks for your reply, I should have been more thoughtful about the > quotations! > I'll put my actual input here: > > &INPUTPP > ! prefix = 'Anatase', > fileout ='out', >output = 'xsf', >outdir = '/scratch/negar/espresso/out/', >lcharge=.TRUE., >lforces=.TRUE., >ldynamics =.False., >lpdb=.TRUE., >lrotation = .False., > ! ns1, ns2, ns3, > ! np1, np2, np3, > ! nframes=50, >ndr=50, > ! ndw=91, >atomic_number(1)=22 >atomic_number(2)=8, > ! charge_density= 'full', >state= 'KS_1', >lbinary=.TRUE. > / > > I'm still getting the same error! and what surprises me is that I have set > the ndr value equal to 50 in both my cp.in and cppp.in and the program is > still looking for cp_51.save! which doesn't exist! (Even if I change the > folder name to 50 manually, that wouldn't change anything!) > > Many thanks, > Nash > > > > > On Mon, Jul 9, 2012 at 2:18 PM, Negar Ashari Astani > wrote: > >> >> Hello everyone, >> >> I'm confronting a probably stupid problem with cppp.x! I saw this problem >> being reported two times in the forum: >> >> http://www.democritos.it/pipermail/pw_forum/2011-February/019298.html >> >> http://www.democritos.it/pipermail/pw_forum/2008-May/009020.html >> >> Having read those, I'm still getting the following error: >> >> Cannot open file espresso/out/cp_51.save/data-file.xml >> >> I checked the corresponding address, and the files are there! >> and I also renamed the save directory and files to match the default >> cp_51 and . >> >> >> This is my input file for cppp.x: >> >> >> &INPUTPP >> ! prefix=Anatase, >>fileout=out, >>output=xsf, >>outdir=..mypath../espresso/out, >>wfcdir=..mypath../espresso/out, >>lcharge=.TRUE., >>lforces=.TRUE., >>ldynamics=.TRUE., >>lpdb=.TRUE., >>lrotation, >>ns1, ns2, ns3, >>np1, np2, np3, >>nframes=50, >> ! ndr=90, >> ! ndw=91, >>atomic_number(1) 22 >>atomic_number(2) 8, >>charge_density, >>state= KS_1, >>lbinary=.TRUE. >> / >> >> Although I'm using Q.Espresso.5, I tried to replace fpmdpp.f90 with the >> file provided by Paolo in the second link! >> That didn't work either! >> >> Many thanks, >> Nash >> >> >> > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/4709a059/attachment.htm
[Pw_forum] segfault in projwfc calculation
Dear all
I'm trying to perform some post-processing calculations with QE 5.0 compiled
against
gfortran 4.4.4 and mkl on a parallel machine. pw.x calculations are OK, as well
as dos.x and pp.x
ones. projwfc.x calculations stop instead without complaining and I found this
system error
mpirun noticed that process rank 2 with PID 12250 on node compute-1-1 exited on
signal 11
(Segmentation fault).
You may perform yourself the calculations, if you want; it's a simple water
molecule in a small box
(O and H can be found in the pseudo library). Any suggestion will be
appreciated...
Giuseppe
export MACHINE_FILE=`pwd`/Machine
export NP=8
export ESPRESSO=/home/mattioligi/5.0-gcc4.4/bin
export PARA_PREFIX="mpirun -machinefile $MACHINE_FILE -np $NP"
export PARA_POSTFIX=
export OMP_NUM_THREADS=1
export FILE="h2o-test"
export INPFILE=$FILE-1.inp
export OUTFILE=$FILE-1.out
echo " $FILE"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
&control
calculation = 'relax'
restart_mode='restart',
prefix='$FILE',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&system
ibrav=1, celldm(1)=10.0,
nat=3, ntyp=2,
ecutwfc=30.0,
ecutrho=180.0,
nspin=1,
/
&electrons
mixing_mode='plain'
mixing_beta=0.3
conv_thr=1.0d-6
electron_maxstep=200
/
&ions
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
O15.999O_pbe.van.UPF
H 1.008H_pbe.van.UPF
ATOMIC_POSITIONS {angstrom}
O2.0 2.0 1.8078189690 0 1
H2.0 2.775615577 1.20 1 0
H2.0 1.224385277 1.20 1 0
K_POINTS {gamma}
EOF
$PARA_PREFIX $ESPRESSO/pw.x -ndiag 4 $PARA_POSTFIX < $INPFILE >> $OUTFILE
export FILEA="$FILE"
export INPFILE=$FILEA-dos.inp
export OUTFILE=$FILEA-dos.out
echo " $FILEA"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
&dos
prefix = '$FILEA'
outdir = '$TMP_DIR/'
fildos='$FILEA.dos'
/
EOF
$PARA_PREFIX $ESPRESSO/dos.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
export INPFILE=$FILEA-pdos.inp
export OUTFILE=$FILEA-pdos.out
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
&projwfc
prefix = '$FILEA'
outdir = '$TMP_DIR/'
filproj='$FILEA.proj'
filpdos='$FILEA.pdos'
/
EOF
$PARA_PREFIX $ESPRESSO/projwfc.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
This is the standard output of the projwfc calculation
Program PROJWFC v.5.0 starts on 10Jul2012 at 12:20: 1
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/quote.php
Parallel version (MPI), running on 8 processors
R & G space division: proc/pool =8
Info: using nr1, nr2, nr3 values from input
Info: using nr1s, nr2s, nr3s values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0)
EXX-fraction =0.00
Any further DFT definition will be discarded
Please, verify this is what you really want
Parallelization info
sticks: dense smooth PW G-vecs:dense smooth PW
Min 178 118 30 5078 2754 346
Max 180 120 31 5084 2773 350
Sum1433 94924140651221192777
Tot 717 475121
negative rho (up, down): 0.186E-02 0.000E+00
Gaussian broadening (default values): ngauss,degauss= 00.000735
Calling pprojwave
gamma-point specific algorithms are used
Problem Sizes
natomwfc =6
nbnd =4
nkstot =1
npwx = 175
nkb = 10
--
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail:
[Pw_forum] U calculation in LDA+U
Thanks Dr. Matteo. That is helpful. On Tue, Jul 10, 2012 at 11:15 AM, Matteo Cococcioni wrote: > Dear Peng, > > let me add one word to Burak's. > you need to distinguish two O kinds anyway, whether you shift the > atomic position or not. if you don't do that you will be perturbing > all the oxygen atoms at the same time. > The necessity to have the perturbed atom described as of a different > type (although with the same pseudopotential) is what makes it > convenient (most of the time) to place it at the origin of the unit > cell. > > best, > > Matteo > > > > On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen > wrote: > > When O is perturbed in the case of NiO in tutorial, it > is re-positioned and > > there are 2 different kinds of O (first with 1 atom, the second with 7 > > atoms). Then the kind with only one O is perturbed. In the tutorial, it > > reads "This is done to preserve the largest possible number of > symmetries". > > Is this process necessary? Can we just run computation without > re-position? > > In that case, there is only one kind of O with 8 atoms. > > > > In the position file "filepos", the scale of cell length is always 10, > even > > if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in > > position file no matter what the real scale is? > > > > On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu > wrote: > >> > >> Hi Peng, > >> > >> r.x assigns the values of the response matrices only by considering the > >> distance between atoms and whether they have the same spin and type or > not. > >> This information has to be given by the user in the positions file > "filepos" > >> read by &input_mat. If B(1) and B(2) are different types > >> (e.g. crystallographically) you should perturb them separately, as you > >> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), > type 2 > >> is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x > >> > >> Best regards, > >> > >> Burak > >> > >> > >> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli < > degironc at sissa.it> > >> wrote: > >>> > >>> I don't know the details of r.x code but I think that, physically, what > >>> matters is the two atoms are crystallographically equivalent or not > >>> .therefore I think space group symmetry is the relevant one. > >>> > >>> stefano > >>> > >>> > >>> On 07/10/2012 05:54 AM, Peng Chen wrote: > >>> > >>> Dear All, > >>> > >>> In the calculation of U, how can we determine the equivalence of the > >>> ions, > >>> by site symmetry or space group symmetry? > >>> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we > >>> run > >>> calculation on perturbing B(1) and B(2) ions or just a B ion? > >>> > >>> In order to find U in B ions, I tried to run calculation with > >>> perturbing > >>> just on B, and r.x gave some errors that it needs to read more data. > >>> So I guess it needs the perturbed data from other atoms. Shall I use > the > >>> procedures listed below? > >>> 1. run scf calculation with Hubbard_U(i)= 1.d-20 > >>> 2. run scf with perturbing on an A ion > >>> 3. run scf with perturbing on a B(1) ion > >>> 4. run scf with perturbing on a B(2) ion > >>> 5. run scf with perturbing on an O ion > >>> > >>> > >>> > >>> > >>> > >>> > >>> ___ > >>> Pw_forum mailing list > >>> Pw_forum at pwscf.org > >>> http://www.democritos.it/mailman/listinfo/pw_forum > >>> > >>> > >>> > >>> > >>> ___ > >>> Pw_forum mailing list > >>> Pw_forum at pwscf.org > >>> http://www.democritos.it/mailman/listinfo/pw_forum > >>> > >> > >> > >> ___ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > > > > -- > > Best Regards. > > Peng > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056Fax +1 612 626 7246 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Regards. Peng -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/5c652eff/attachment-0001.htm
[Pw_forum] confused by electron-phonon coupling recover
Dear all? Sorry for interruption .I am confused for two months by the recover problem of Aluminum electron phonon coupling calculation . As we all know,the most time-consuming part of the calculation is the running of ph.x program. Ph.x can not complet all the q vetors in one job time due to the jobtime limit of our machine .What I can do is to submit job for the second time with "recover=.true." setted in ph.in file (the input file for ph.x grogram) .then go on the calculation of q2r.x and matdyn.x .It is obvious that the result is not rational because both e-p coupling strength and Eliashberg function is ZERO. The attachment is all my input file for e-p calculation . It will be very gratefull if you will be kind enough to give me some hints ,I am dying ,help me ,please best regards !! Jianyong Chen institue of physics Chines academy of science -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: matdyn.in Type: application/octet-stream Size: 3117 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: matdynep.in Type: application/octet-stream Size: 156 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: ph.in Type: application/octet-stream Size: 227 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: q2r.in Type: application/octet-stream Size: 73 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment-0003.obj -- next part -- A non-text attachment was scrubbed... Name: run Type: application/octet-stream Size: 310 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment-0004.obj -- next part -- A non-text attachment was scrubbed... Name: scf1.in Type: application/octet-stream Size: 412 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment-0005.obj -- next part -- A non-text attachment was scrubbed... Name: scf2.in Type: application/octet-stream Size: 411 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120710/d27fb6af/attachment-0006.obj
[Pw_forum] Memory (RAM)
On Jul 9, 2012, at 23:43 , Vo, Trinh (388C) wrote: > I am running very large job (nscf calculation 15x15x15) using QE > version 4.3.2. > The job keeps being crashed due to memory problem (out of memory, > RAM). > Is there a way that I can estimate how much memory (RAM) required > for running > a nscf calculation? some explanations here: http://www.quantum-espresso.org/wp-content/uploads/Doc/ pw_user_guide/node13.html Note that a large number of k-points does not imply a large RAM, but a large number of bands does. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?
Dear Eduardo, thanks for your consideration on my problem, Bests. Yavar -Original Message- From: Eduardo Ariel Menendez Proupin To: pw_forum at pwscf.org Date: Mon, 9 Jul 2012 09:44:20 +0200 Subject: Re: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP? Dear Yavar USPP and NCPP are mathematical methods to approximate the solution of the same physical problem. Hence, there must be no physically different results, unless one of the pseudopotentials is faulty. Both types of pseudopotentials have cutoff radii, which are larger for NCPP than for USPP. The wavefunctions computed with any pseudopotential should be equal to the all-electron wavefunctions in the spatial region outside the spheres centered at each atom with spheres radii equal to the cutoff radii of the corresponding pseudopotential. Inside any sphere, the wavefunctions are different and are meaningless. To have the correct wavefunctions inside the spheres you have any of the following options a) all-electron calculations (with a different code,e.g. ADF, Gaussian, LMTO, etc), b) use a PP with a smaller cutoff radius (and larger ecutrho and ecutwfc), c) use PAW (projector augmented wave). sincerely yours Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 Dear QE users. I want to plot HOMO, LUMO isosurfaces. what is the physical origin of difference between results from choosing USPP with NCPP? Thanks in advance. --- Yavar Taghipour Azar PhD Student Physics Group, AEOI Tehran-Iran Email: ytaghipour at aeoi.org.ir Phone: +98 (0) 21 82064556 --- -- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/69d1a228/attachment.htm
[Pw_forum] U calculation in LDA+U
Thanks Burak. I appreciate your suggestions and I will try. On Tue, Jul 10, 2012 at 11:11 AM, Burak Himmetoglu wrote: > Hi Peng, > > In my experience, the process of shifting the O atom to the origin is > recommended since it produces more stable results numerically, especially > in the second part of r.x where the program extrapolates to larger > supercells using the results from the starting supercell you have used. > However, if the crystal has already very small number of symmetries, then > you should be able to avoid this shifting. > > The first three entries in filepos are the lattice vectors in units of > alat (like the CELL_PARAMETERS when ibrav=0). The unit cell is expanded by > a factor of 10 in the tutorial. The length scale in filepos is not > necessary. That file is used only to compare the distances between pairs of > atoms and the scale does not really matter. It is generally better to scale > up only for numerical stability reasons. > > Best regards, > > Burak > > On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen wrote: > >> When O is perturbed in the case of NiO in tutorial, it >> is re-positioned and there are 2 different kinds of O (first with 1 atom, >> the second with 7 atoms). Then the kind with only one O is perturbed. In >> the tutorial, it reads "This is done to preserve the largest possible >> number of symmetries". Is this process necessary? Can we just run >> computation without re-position? In that case, there is only one kind of O >> with 8 atoms. >> >> In the position file "filepos", the scale of cell length is always 10, >> even if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in >> position file no matter what the real scale is? >> >> On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu wrote: >> >>> Hi Peng, >>> >>> r.x assigns the values of the response matrices only by considering the >>> distance between atoms and whether they have the same spin and type or not. >>> This information has to be given by the user in the positions file >>> "filepos" read by &input_mat. If B(1) and B(2) are different types >>> (e.g. crystallographically) you should perturb them separately, as you >>> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type >>> 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x >>> >>> Best regards, >>> >>> Burak >>> >>> >>> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli >> > wrote: >>> >>>> I don't know the details of r.x code but I think that, physically, >>>> what matters is the two atoms are crystallographically equivalent or not >>>> .therefore I think space group symmetry is the relevant one. >>>> >>>> stefano >>>> >>>> >>>> On 07/10/2012 05:54 AM, Peng Chen wrote: >>>> >>>> Dear All, >>>> >>>> In the calculation of U, how can we determine the equivalence of the ions, >>>> by site symmetry or space group symmetry? >>>> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run >>>> calculation on perturbing B(1) and B(2) ions or just a B ion? >>>> >>>> In order to find U in B ions, I tried to run calculation with perturbing >>>> just on B, and r.x gave some errors that it needs to read more data. >>>> So I guess it needs the perturbed data from other atoms. Shall I use the >>>> procedures listed below? >>>> 1. run scf calculation with Hubbard_U(i)= 1.d-20 >>>> 2. run scf with perturbing on an A ion >>>> 3. run scf with perturbing on a B(1) ion >>>> 4. run scf with perturbing on a B(2) ion >>>> 5. run scf with perturbing on an O ion >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> ___ >>>> Pw_forum mailing listPw_forum at >>>> pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>>> >>>> >>>> ___ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> Best Regards. >> Peng >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/8f7f608b/attachment.htm
[Pw_forum] HOMO,LUMO isosurface, USPP or NCPP?
-Original Message- From: Eduardo Ariel Menendez Proupin To: pw_forum at pwscf.org Date: Mon, 9 Jul 2012 09:44:20 +0200 Subject: Re: [Pw_forum] HOMO,LUMO isosurface, USPP or NCPP? > Dear Yavar > > USPP and NCPP are mathematical methods to approximate the solution of > the > same physical problem. Hence, there must be no physically different > results, unless one of the pseudopotentials is faulty. Both types of > pseudopotentials have cutoff radii, which are larger for NCPP than for > USPP. The wavefunctions computed with any pseudopotential should be > equal > to the all-electron wavefunctions in the spatial region outside the > spheres > centered at each atom with spheres radii equal to the cutoff radii of > the > corresponding pseudopotential. Inside any sphere, the wavefunctions are > different and are meaningless. To have the correct wavefunctions inside > the > spheres you have any of the following options a) all-electron > calculations > (with a different code,e.g. ADF, Gaussian, LMTO, etc), b) use a PP with > a > smaller cutoff radius (and larger ecutrho and ecutwfc), c) use PAW > (projector augmented wave). > > sincerely yours > > > Eduardo Menendez Proupin > Departamento de Qu?mica Fisica Aplicada > Facultad de Ciencias > Universidad Aut?noma de Madrid > 28049 Madrid, Spain > Phone: +34 91 497 6706 > > > > Dear QE users. > > > > > > I want to plot HOMO, LUMO isosurfaces. what is the physical origin > > of difference between results from choosing USPP with NCPP? > > Thanks in advance. > > > > > > --- > > Yavar Taghipour Azar > > PhD Student > > Physics Group, AEOI > > Tehran-Iran > > > > Email: ytaghipour at aeoi.org.ir > > Phone: +98 (0) 21 82064556 > > --- > > > > > > > > > > > -- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/c54a5751/attachment-0001.htm
[Pw_forum] Error #19 MoS2 ecutoff convergence test
On Tue, Jul 10, 2012 at 11:09 AM, Sohail Ahmad wrote: > nband = 10, > > This should be nbnd = 10, best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/4e555d23/attachment.htm
[Pw_forum] pwcond transmission tran_file
Hi all, This question should probably be directed to Alexander Smogunov, as it is about the pwcond code. I'm currently doing some transport calculations with FeCo / MgO systems - I'm getting expected results using a 4 layer MgO, however, I want to compare to larger barrier widths, but the total transmissions given in the tran_file are small, and I require more than the seven decimal limit for the minority channel transmissions results. Can you tell me where in the code I can extend the output for the tran_file so I can see results to greater than seven decimal places? Thanks, Jonathan -- Jonathan Trinastic, M.S. Graduate Student Department of Physics University of Florida
[Pw_forum] GRID example of e-ph
On Tue, 2012-07-10 at 09:33 +0800, Peng Tao wrote: > Dear all, > > > As we know, the phonon calculation is quite slow and unexpected errors > might occur at any time. > Thanks to the GRID example, split runs is available. However, no > example is provided to split > the e-ph calculation. So, dear professors, could you show me a method > to realize it? > PHonon/examples/GRID_example/run_example_2 in QE 5.0. HTH Andrea > Sincerely yours > Plato Tao > > -- > --- > PH.D. candidate Peng Tao > Magnetism and Magnetic Materials Division > National Laboratory for Material Science > Institute of Metal Research, Chinese Academy of Sciences > Phone +86-024-83978751 > --- > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal CorsoTel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
[Pw_forum] U calculation in LDA+U
When O is perturbed in the case of NiO in tutorial, it is re-positioned and there are 2 different kinds of O (first with 1 atom, the second with 7 atoms). Then the kind with only one O is perturbed. In the tutorial, it reads "This is done to preserve the largest possible number of symmetries". Is this process necessary? Can we just run computation without re-position? In that case, there is only one kind of O with 8 atoms. In the position file "filepos", the scale of cell length is always 10, even if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in position file no matter what the real scale is? On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu wrote: > Hi Peng, > > r.x assigns the values of the response matrices only by considering the > distance between atoms and whether they have the same spin and type or not. > This information has to be given by the user in the positions file > "filepos" read by &input_mat. If B(1) and B(2) are different types > (e.g. crystallographically) you should perturb them separately, as you > outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type > 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x > > Best regards, > > Burak > > > On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli sissa.it>wrote: > >> I don't know the details of r.x code but I think that, physically, what >> matters is the two atoms are crystallographically equivalent or not >> .therefore I think space group symmetry is the relevant one. >> >> stefano >> >> >> On 07/10/2012 05:54 AM, Peng Chen wrote: >> >> Dear All, >> >> In the calculation of U, how can we determine the equivalence of the ions, >> by site symmetry or space group symmetry? >> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run >> calculation on perturbing B(1) and B(2) ions or just a B ion? >> >> In order to find U in B ions, I tried to run calculation with perturbing >> just on B, and r.x gave some errors that it needs to read more data. >> So I guess it needs the perturbed data from other atoms. Shall I use the >> procedures listed below? >> 1. run scf calculation with Hubbard_U(i)= 1.d-20 >> 2. run scf with perturbing on an A ion >> 3. run scf with perturbing on a B(1) ion >> 4. run scf with perturbing on a B(2) ion >> 5. run scf with perturbing on an O ion >> >> >> >> >> >> >> >> ___ >> Pw_forum mailing listPw_forum at >> pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/140dfec6/attachment.htm
[Pw_forum] U calculation in LDA+U
Dear Peng, let me add one word to Burak's. you need to distinguish two O kinds anyway, whether you shift the atomic position or not. if you don't do that you will be perturbing all the oxygen atoms at the same time. The necessity to have the perturbed atom described as of a different type (although with the same pseudopotential) is what makes it convenient (most of the time) to place it at the origin of the unit cell. best, Matteo On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen wrote: > When O is perturbed in the case of NiO in tutorial, it is?re-positioned?and > there are 2 different kinds of O (first with 1 atom, the second with 7 > atoms).??Then the kind with only one O is perturbed. In the tutorial, it > reads "This is done to preserve the largest possible number of symmetries". > ?Is this process necessary? Can we just run computation without re-position? > In that case, there is only one kind of O with 8 atoms. > > In the position file "filepos", the scale of cell length is always 10, even > if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in > position file no matter what the real scale is? > > On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu wrote: >> >> Hi Peng, >> >> r.x assigns the values of the response matrices only by considering the >> distance between atoms and whether they have the same spin and type or not. >> This information has to be given by the user in the positions file "filepos" >> read by &input_mat.?If B(1) and B(2) are different types >> (e.g.?crystallographically)?you should perturb them?separately, as you >> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type 2 >> is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x >> >> Best regards, >> >> Burak >> >> >> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli >> wrote: >>> >>> I don't know the details of r.x code but I think that, physically, what >>> matters is the two atoms are crystallographically equivalent or not >>> .therefore I think space group symmetry is the relevant one. >>> >>> stefano >>> >>> >>> On 07/10/2012 05:54 AM, Peng Chen wrote: >>> >>> Dear All, >>> >>> In the calculation of U, how can we determine the equivalence of the >>> ions, >>> by site symmetry or space group symmetry? >>> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we >>> run >>> calculation on perturbing B(1) and B(2) ions or just a B ion? >>> >>> In order to find U in B ions, I tried to run calculation with >>> perturbing >>> just on B, and r.x gave some errors that it needs to read more data. >>> So I guess it needs the perturbed data from other atoms. Shall I use the >>> procedures listed below? >>> 1. run scf calculation with Hubbard_U(i)= 1.d-20 >>> 2. run scf with perturbing on an A ion >>> 3. run scf with perturbing on a B(1) ion >>> 4. run scf with perturbing on a B(2) ion >>> 5. run scf with perturbing on an O ion >>> >>> >>> >>> >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > ? Best Regards. > ? ? ? ? Peng > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 ? ?Fax +1 612 626 7246
[Pw_forum] U calculation in LDA+U
Hi Peng, In my experience, the process of shifting the O atom to the origin is recommended since it produces more stable results numerically, especially in the second part of r.x where the program extrapolates to larger supercells using the results from the starting supercell you have used. However, if the crystal has already very small number of symmetries, then you should be able to avoid this shifting. The first three entries in filepos are the lattice vectors in units of alat (like the CELL_PARAMETERS when ibrav=0). The unit cell is expanded by a factor of 10 in the tutorial. The length scale in filepos is not necessary. That file is used only to compare the distances between pairs of atoms and the scale does not really matter. It is generally better to scale up only for numerical stability reasons. Best regards, Burak On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen wrote: > When O is perturbed in the case of NiO in tutorial, it > is re-positioned and there are 2 different kinds of O (first with 1 atom, > the second with 7 atoms). Then the kind with only one O is perturbed. In > the tutorial, it reads "This is done to preserve the largest possible > number of symmetries". Is this process necessary? Can we just run > computation without re-position? In that case, there is only one kind of O > with 8 atoms. > > In the position file "filepos", the scale of cell length is always 10, > even if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in > position file no matter what the real scale is? > > On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu wrote: > >> Hi Peng, >> >> r.x assigns the values of the response matrices only by considering the >> distance between atoms and whether they have the same spin and type or not. >> This information has to be given by the user in the positions file >> "filepos" read by &input_mat. If B(1) and B(2) are different types >> (e.g. crystallographically) you should perturb them separately, as you >> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type >> 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x >> >> Best regards, >> >> Burak >> >> >> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli > sissa.it>wrote: >> >>> I don't know the details of r.x code but I think that, physically, >>> what matters is the two atoms are crystallographically equivalent or not >>> .therefore I think space group symmetry is the relevant one. >>> >>> stefano >>> >>> >>> On 07/10/2012 05:54 AM, Peng Chen wrote: >>> >>> Dear All, >>> >>> In the calculation of U, how can we determine the equivalence of the ions, >>> by site symmetry or space group symmetry? >>> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run >>> calculation on perturbing B(1) and B(2) ions or just a B ion? >>> >>> In order to find U in B ions, I tried to run calculation with perturbing >>> just on B, and r.x gave some errors that it needs to read more data. >>> So I guess it needs the perturbed data from other atoms. Shall I use the >>> procedures listed below? >>> 1. run scf calculation with Hubbard_U(i)= 1.d-20 >>> 2. run scf with perturbing on an A ion >>> 3. run scf with perturbing on a B(1) ion >>> 4. run scf with perturbing on a B(2) ion >>> 5. run scf with perturbing on an O ion >>> >>> >>> >>> >>> >>> >>> >>> ___ >>> Pw_forum mailing listPw_forum at >>> pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Best Regards. > Peng > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/947ce6f7/attachment.htm
[Pw_forum] U calculation in LDA+U
Thanks stefano and Burak. If space group matters, then the 3 types will be A, B and O. On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu wrote: > Hi Peng, > > r.x assigns the values of the response matrices only by considering the > distance between atoms and whether they have the same spin and type or not. > This information has to be given by the user in the positions file > "filepos" read by &input_mat. If B(1) and B(2) are different types > (e.g. crystallographically) you should perturb them separately, as you > outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type > 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x > > Best regards, > > Burak > > > On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli sissa.it>wrote: > >> I don't know the details of r.x code but I think that, physically, what >> matters is the two atoms are crystallographically equivalent or not >> .therefore I think space group symmetry is the relevant one. >> >> stefano >> >> >> On 07/10/2012 05:54 AM, Peng Chen wrote: >> >> Dear All, >> >> In the calculation of U, how can we determine the equivalence of the ions, >> by site symmetry or space group symmetry? >> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run >> calculation on perturbing B(1) and B(2) ions or just a B ion? >> >> In order to find U in B ions, I tried to run calculation with perturbing >> just on B, and r.x gave some errors that it needs to read more data. >> So I guess it needs the perturbed data from other atoms. Shall I use the >> procedures listed below? >> 1. run scf calculation with Hubbard_U(i)= 1.d-20 >> 2. run scf with perturbing on an A ion >> 3. run scf with perturbing on a B(1) ion >> 4. run scf with perturbing on a B(2) ion >> 5. run scf with perturbing on an O ion >> >> >> >> >> >> >> >> ___ >> Pw_forum mailing listPw_forum at >> pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best Regards. Peng -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/c8eb7a6a/attachment.htm
[Pw_forum] GRID example of e-ph
Dear all, As we know, the phonon calculation is quite slow and unexpected errors might occur at any time. Thanks to the GRID example, split runs is available. However, no example is provided to split the e-ph calculation. So, dear professors, could you show me a method to realize it? Sincerely yours Plato Tao -- --- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/65855266/attachment.htm
[Pw_forum] regarding phonon dispersion
Dear all, I am running phonon dispersion for YSn3, which is crystallizes in cubic structure. While running the programme i dont have any imaginary frequencies in my o/p file (ph.out). But using plotband.x tool for plotting dispersion, my final plot got negative axis exactly starting from the value of Fermi energy. Below i am sending the plotband.x details Reading 12 bands at101 k-points Range:0. 133.5007eV Emin, Emax > 0 140 high-symmetry point: 0. 0. 0. x coordinate 0. high-symmetry point: 0.5000 0. 0. x coordinate 0.5000 high-symmetry point: 0.5000 0.5000 0. x coordinate 1. high-symmetry point: 0. 0. 0. x coordinate 1.7071 high-symmetry point: 0.5000 0.5000 0.5000 x coordinate 2.5731 high-symmetry point: 0.5000-0.5000 0.5000 x coordinate 3.5731 high-symmetry point: 0. 0. 0.5000 x coordinate 4.2802 output file (xmgr) > YSn3.xmgr bands in xmgr format written to file YSn3.xmgr output file (ps) > YSn3.ps Efermi > 13.2559 deltaE, reference E (for tics) 30, 13.2559 bands in PostScript format written to file YSn3.ps . Is there any error in my calculation or any bug in plotband.x. Because the same o/p YSn3.xmgr from this plotband.x shows nicely with xmgrce shows. please help me in this. Thanks in advance S.Appalakondaiah Research scholar University of Hyderabad Hyderabad India -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/7593bf8e/attachment-0001.htm
[Pw_forum] phonon eigenvector units
Hello,
I have performed a phonon calculation using ph.x. During the scf calculation
(prior to using ph.x), the ATOMIC_POSITIONS is in Bohr units. I am also using
ibrav = 0 and an orthorhombic crystal system. After ph.x, I have used dynmat.x
to apply asymmetric sum rule and ?get the new phonon eigenvalues and
eigenvectors. The output of dynmat.x has the following format:?
? ? ?omega(12) = ? ? ? 1.305968 [THz] = ? ? ?43.562397 [cm-1]
?( -0.052340 ? 0.00 ? ?-0.021008 ? 0.00 ? ? 0.002346 ? 0.00 ? )
?( -0.003841 ? 0.00 ? ?-0.009204 ? 0.00 ? ? 0.053835 ? 0.00 ? )
?( ?0.014655 ? 0.00 ? ?-0.015822 ? 0.00 ? ? 0.085998 ? 0.00 ? )
?( -0.013791 ? 0.00 ? ?-0.035434 ? 0.00 ? ? 0.066956 ? 0.00 ? )
While the units of omega is evident, the unit of eigenvectors is not clear. I
wonder what is the unit of eigenvectors ?
The atomic position have the following units:
ATOMIC_POSITIONS { alat | bohr | crystal | angstrom }
Do the phonon eigenvectors have the same units as atomic positions or they have
one particular unit always ? If it is one particular unit then what it is ? I
noticed that the dynamical matrix is written in cartesian axes (I assume it
means ?in the units of alat).?
Thanks,
David
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[Pw_forum] U calculation in LDA+U
I don't know the details of r.x code but I think that, physically, what matters is the two atoms are crystallographically equivalent or not .therefore I think space group symmetry is the relevant one. stefano On 07/10/2012 05:54 AM, Peng Chen wrote: > Dear All, > > In the calculation of U, how can we determine the equivalence of the ions, > by site symmetry or space group symmetry? > E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run > calculation on perturbing B(1) and B(2) ions or just a B ion? > > In order to find U in B ions, I tried to run calculation with perturbing > just on B, and r.x gave some errors that it needs to read more data. > So I guess it needs the perturbed data from other atoms. Shall I use the > procedures listed below? > 1. run scf calculation with Hubbard_U(i)= 1.d-20 > 2. run scf with perturbing on an A ion > 3. run scf with perturbing on a B(1) ion > 4. run scf with perturbing on a B(2) ion > 5. run scf with perturbing on an O ion > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/0a5535ed/attachment.htm
[Pw_forum] regarding phonon dispersion
On Tue, Jul 10, 2012 at 5:53 AM, Kondaiah Samudrala wrote: > Dear all, > > I am running phonon dispersion for YSn3, which is crystallizes in cubic > structure. While running the programme i dont have any imaginary > frequencies in my o/p file (ph.out). But using plotband.x tool for > plotting dispersion, my final plot got negative axis exactly starting from > the value of Fermi energy. Below i am sending the plotband.x details > > Dear Kondaiah, plotband.x was written to plot electronic bands, hence it sets the energy zero at the "Fermu energy" level specified in input. When using it to plot phonon bands, just set Efermi to zero. bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/129e10a6/attachment.htm
[Pw_forum] U calculation in LDA+U
Hi Peng, r.x assigns the values of the response matrices only by considering the distance between atoms and whether they have the same spin and type or not. This information has to be given by the user in the positions file "filepos" read by &input_mat. If B(1) and B(2) are different types (e.g. crystallographically) you should perturb them separately, as you outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type 2 is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x Best regards, Burak On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli wrote: > I don't know the details of r.x code but I think that, physically, what > matters is the two atoms are crystallographically equivalent or not > .therefore I think space group symmetry is the relevant one. > > stefano > > > On 07/10/2012 05:54 AM, Peng Chen wrote: > > Dear All, > > In the calculation of U, how can we determine the equivalence of the ions, > by site symmetry or space group symmetry? > E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we run > calculation on perturbing B(1) and B(2) ions or just a B ion? > > In order to find U in B ions, I tried to run calculation with perturbing > just on B, and r.x gave some errors that it needs to read more data. > So I guess it needs the perturbed data from other atoms. Shall I use the > procedures listed below? > 1. run scf calculation with Hubbard_U(i)= 1.d-20 > 2. run scf with perturbing on an A ion > 3. run scf with perturbing on a B(1) ion > 4. run scf with perturbing on a B(2) ion > 5. run scf with perturbing on an O ion > > > > > > > > ___ > Pw_forum mailing listPw_forum at > pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120710/aaf8c364/attachment.htm
