[Pw_forum] error in charge density difference (chden.f90)
Juliana Mendes
mendesjuliana.juli at gmail.com
Thu Sep 24 13:19:38 CEST 2015
Thank you for your help Paolo. Have a nice day!
Juliana de O. Mendes
Postdoctoral in Chemistry
Physical Chemistry Department
Chemistry Institute
Federal University of Rio de Janeiro
Cidade Universitária, CT Bloco A sala 412
Rio de Janeiro, RJ 21949-900
Brazil
2015-09-24 7:00 GMT-03:00 <pw_forum-request at pwscf.org>:
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> Today's Topics:
>
> 1. Re: ibrav = 13 monoclinic-base-centered unique axis
> (Andrea Dal Corso)
> 2. error in charge density difference (chden.f90) (Juliana Mendes)
> 3. Re: error in charge density difference (chden.f90)
> (Paolo Giannozzi)
> 4. Re: Problem in average.x (Huang, Xu)
> 5. Temperature effect on band gap (reza vatan)
> 6. tetragonal lamno3 (Jaret Qi)
> 7. Monolayer MoS2 band Structure (Cameron Foss)
> 8. Re: Temperature effect on band gap (Lorenzo Paulatto)
> 9. Mean internal potential for e-microscopy
> (Cristian Degli Esposti Boschi)
> 10. Re: Monolayer MoS2 band Structure (Thomas Brumme)
> 11. Re: Monolayer MoS2 band Structure (Giovanni Cantele)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 Sep 2015 13:57:28 +0200
> From: Andrea Dal Corso <dalcorso at sissa.it>
> Subject: Re: [Pw_forum] ibrav = 13 monoclinic-base-centered unique
> axis
> To: pw_forum at pwscf.org
> Message-ID: <1443009448.14190.7.camel at ulisse.cm.sissa.it>
> Content-Type: text/plain; charset="UTF-8"
>
> In recent versions of QE
>
> ibrav=-13
>
> is allowed for b-unique base centered monoclinic.
>
> HTH,
>
> Andrea
>
> On Wed, 2015-09-23 at 11:17 +0200, Ludwig, Stephan wrote:
> > Hello,
> >
> > ?
> >
> > I want to work on a salt with space group monoclinic-base centered. This
> means ibrav=13 in th input file.
> >
> > For simple monoclinic lattices there are two distinct possibilties to
> choose the unique axis (ibrav=12 or -12).
> >
> > Ibrav=13 obviously chooses the c-axis to be the unique one.
> >
> > Is there a possibility to choose the b-axis to be unique?
> >
> >
> >
> > Thanks and regards
> >
> >
> >
> > Stephan
> >
> > ?
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Andrea Dal Corso Tel. 0039-040-3787428
> SISSA, Via Bonomea 265 Fax. 0039-040-3787249
> I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 23 Sep 2015 09:38:36 -0300
> From: Juliana Mendes <mendesjuliana.juli at gmail.com>
> Subject: [Pw_forum] error in charge density difference (chden.f90)
> To: pw_forum <pw_forum at pwscf.org>
> Message-ID:
> <
> CAGJDPkr5Uzygux7M4FjDRJcED6DeDhB_0UtO8ZPDhJh2MsSCDg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Pwscf users,
>
> I am trying to do a charge density difference plot of my system (an organic
> molecule adsorbed on iron (001)), but I'm finding the following problem
> when I run the pp.x code.
>
>
> Currently Loaded Modulefiles:
> 1) softwares/intel/11.0/schrodinger/2012-04
> 2) compiladores/intel/2011
> 3) bibliotecas/intel/2011/openmpi/1.4.5
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 5390 on
> node compute-3-1.local exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
>
> I am working with 4 processors (all calculations) and my version of quantum
> espresso is 5.0. I tried in different machines to check if the problem was
> in my machine, but I still have the same problem.
> I don't know if the problem is in my machines, in the QE version or if it
> is a compilation problem.
>
> Below is attached my input:
>
> &inputpp
> /
> &plot
> nfile=3
> filepp(1)='imidza.perp.hollow.mag141.charge', weight(1)=1.0
> filepp(2)='sup63.opt.mag141.charge', weight(2)=-1.0
> filepp(3)='imidza.perp.hollow.charge', weight(3)=-1.0
> iflag=3
> output_format=5
> fileout='sup.imidza.cdd.xsf'
> /
>
> *Does anyone have an idea of what is happening? *
>
> Thanks in advance for the help!
>
> Regards,
>
> Juliana Mendes.
>
>
> --
>
> Juliana de O. Mendes
>
> Postdoctoral in Chemistry
>
> Physical Chemistry Department
> Chemistry Institute
> Federal University of Rio de Janeiro
> Cidade Universit?ria, CT Bloco A sala 412
> Rio de Janeiro, RJ 21949-900
> Brazil
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> ------------------------------
>
> Message: 3
> Date: Wed, 23 Sep 2015 15:15:06 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] error in charge density difference (chden.f90)
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCuVk9HK62OENxoT5-mLTRGgh2DoGFH=
> E-LMtriD-dLdKA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> The segmentation violation happens at line 84 of flib/plot_io.f90, which
> should be this one:
> read (iunplot, * ) (plot (ir), ir = 1, nr1x * nr2x * nr3)
> Likely it is an out-of-bound error. Use pp.x in serial execution,
> especially whne you produce files containing intermediate results (I think
> the code crashes when reading one of those)
>
> Paolo
>
> On Wed, Sep 23, 2015 at 2:38 PM, Juliana Mendes <
> mendesjuliana.juli at gmail.com> wrote:
>
> > Dear Pwscf users,
> >
> > I am trying to do a charge density difference plot of my system (an
> > organic molecule adsorbed on iron (001)), but I'm finding the following
> > problem when I run the pp.x code.
> >
> >
> > Currently Loaded Modulefiles:
> > 1) softwares/intel/11.0/schrodinger/2012-04
> > 2) compiladores/intel/2011
> > 3) bibliotecas/intel/2011/openmpi/1.4.5
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image PC Routine Line
> > Source
> > pp.x 00000000008A56F4 Unknown Unknown
> Unknown
> > pp.x 00000000008A02C2 Unknown Unknown
> Unknown
> > pp.x 000000000084A766 Unknown Unknown
> Unknown
> > pp.x 00000000008499D7 Unknown Unknown
> Unknown
> > pp.x 0000000000761932 plot_io_ 84
> > plot_io.f90
> > pp.x 0000000000433D35 chdens_ 258
> > chdens.f90
> > pp.x 000000000043233B MAIN__ 44
> > postproc.f90
> > pp.x 0000000000431B5C Unknown Unknown
> Unknown
> > libc.so.6 000000356B41D994 Unknown Unknown
> Unknown
> > pp.x 0000000000431A69 Unknown Unknown
> Unknown
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image PC Routine Line
> > Source
> > pp.x 00000000008A56F4 Unknown Unknown
> Unknown
> > pp.x 00000000008A02C2 Unknown Unknown
> Unknown
> > pp.x 000000000084A766 Unknown Unknown
> Unknown
> > pp.x 00000000008499D7 Unknown Unknown
> Unknown
> > pp.x 0000000000761932 plot_io_ 84
> > plot_io.f90
> > pp.x 0000000000433D35 chdens_ 258
> > chdens.f90
> > pp.x 000000000043233B MAIN__ 44
> > postproc.f90
> > pp.x 0000000000431B5C Unknown Unknown
> Unknown
> > libc.so.6 000000356B41D994 Unknown Unknown
> Unknown
> > pp.x 0000000000431A69 Unknown Unknown
> Unknown
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image PC Routine Line
> > Source
> > pp.x 00000000008A56F4 Unknown Unknown
> Unknown
> > pp.x 00000000008A02C2 Unknown Unknown
> Unknown
> > pp.x 000000000084A766 Unknown Unknown
> Unknown
> > pp.x 00000000008499D7 Unknown Unknown
> Unknown
> > pp.x 0000000000761932 plot_io_ 84
> > plot_io.f90
> > pp.x 0000000000433D35 chdens_ 258
> > chdens.f90
> > pp.x 000000000043233B MAIN__ 44
> > postproc.f90
> > pp.x 0000000000431B5C Unknown Unknown
> Unknown
> > libc.so.6 000000356B41D994 Unknown Unknown
> Unknown
> > pp.x 0000000000431A69 Unknown Unknown
> Unknown
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image PC Routine Line
> > Source
> > pp.x 00000000008A56F4 Unknown Unknown
> Unknown
> > pp.x 00000000008A02C2 Unknown Unknown
> Unknown
> > pp.x 000000000084A766 Unknown Unknown
> Unknown
> > pp.x 00000000008499D7 Unknown Unknown
> Unknown
> > pp.x 0000000000761932 plot_io_ 84
> > plot_io.f90
> > pp.x 0000000000433D35 chdens_ 258
> > chdens.f90
> > pp.x 000000000043233B MAIN__ 44
> > postproc.f90
> > pp.x 0000000000431B5C Unknown Unknown
> Unknown
> > libc.so.6 000000356B41D994 Unknown Unknown
> Unknown
> > pp.x 0000000000431A69 Unknown Unknown
> Unknown
> >
> --------------------------------------------------------------------------
> > mpirun has exited due to process rank 0 with PID 5390 on
> > node compute-3-1.local exiting without calling "finalize". This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpirun (as reported here).
> >
> --------------------------------------------------------------------------
> >
> > I am working with 4 processors (all calculations) and my version of
> > quantum espresso is 5.0. I tried in different machines to check if the
> > problem was in my machine, but I still have the same problem.
> > I don't know if the problem is in my machines, in the QE version or if it
> > is a compilation problem.
> >
> > Below is attached my input:
> >
> > &inputpp
> > /
> > &plot
> > nfile=3
> > filepp(1)='imidza.perp.hollow.mag141.charge', weight(1)=1.0
> > filepp(2)='sup63.opt.mag141.charge', weight(2)=-1.0
> > filepp(3)='imidza.perp.hollow.charge', weight(3)=-1.0
> > iflag=3
> > output_format=5
> > fileout='sup.imidza.cdd.xsf'
> > /
> >
> > *Does anyone have an idea of what is happening? *
> >
> > Thanks in advance for the help!
> >
> > Regards,
> >
> > Juliana Mendes.
> >
> >
> > --
> >
> > Juliana de O. Mendes
> >
> > Postdoctoral in Chemistry
> >
> > Physical Chemistry Department
> > Chemistry Institute
> > Federal University of Rio de Janeiro
> > Cidade Universit?ria, CT Bloco A sala 412
> > Rio de Janeiro, RJ 21949-900
> > Brazil
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> -------------- next part --------------
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> ------------------------------
>
> Message: 4
> Date: Wed, 23 Sep 2015 15:45:40 +0000
> From: "Huang, Xu" <xu-huang at uiowa.edu>
> Subject: Re: [Pw_forum] Problem in average.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <AB771766B61B1E41A254D6940336D4FC7B0DF13F at ITSNT439.iowa.uiowa.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I changed the ppn down to 1 and restart the last part. It's successful and
> finished just in a few seconds. Thank you very much!
>
> Xu Huang
> ________________________________
> From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf
> of Giovanni Cantele [giovanni.cantele at spin.cnr.it]
> Sent: Wednesday, September 23, 2015 2:45 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Problem in average.x
>
> Try to relaunch it on just one processor, usually it is very fast and it
> does not require parallelization.
>
> Giovanni
>
>
> On 23 Sep 2015, at 00:06, Huang, Xu <xu-huang at uiowa.edu<mailto:
> xu-huang at uiowa.edu>> wrote:
>
> Dear all,
>
> I'm using QE to plot the layer-averaged potential for hematite (Fe2O3)
> surface slabs. I did scf (pw.x) first, then got the potential (pp.x), and
> finally tried to make layer-averaged potential (average.x) along surface
> normal. The first 2 steps were successful and finished in ~10 minutes. But
> in the last step, the output file of average.x just stopped at the
> beginning for several days without any new update like this:
> ----------------------
> Program AVERAGE v.5.1.1 starts on 20Sep2015 at 16:58:27
>
> 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<
> http://www.quantum-espresso.org/>",
> in publications or presentations arising from this work. More details
> at
> http://www.quantum-espresso.org/quote
>
> Parallel version (MPI), running on 16 processors
> R & G space division: proc/nbgrp/npool/nimage = 16
> Reading header from file Fe2O3.potential
>
> Info: using nr1, nr2, nr3 values from input
>
> Info: using nr1s, nr2s, nr3s values from input
> ----------------------
>
> And currently the all the files in the working directory are:
> 2779 Sep 20 16:48 QEneonscript_pot_avg
> 2 Sep 20 16:49 results
> 2150 Sep 20 16:49 Fe2O3.scf.in
> 19 Sep 20 16:58 temp
> 127237 Sep 20 16:58 Fe2O3.scf.out
> 138 Sep 20 16:58 Fe2O3.pp.in
> 16051771 Sep 20 16:58 Fe2O3.potential
> 2263 Sep 20 16:58 Fe2O3.pp.out
> 39 Sep 20 16:58 Fe2O3.avg.in
> 696 Sep 20 16:59 Fe2O3.avg.out
>
> I'm very confused about it. I don't know if I missed anything in the
> script for the last step. Here I added the entire run script
> (QEneonscript_pot_avg) of this calculation with all 3 steps below. Thank
> you very much for helping me with this!
>
> Regards,
> Xu Huang
>
> Below is the QEneonscript_pot_avg file:
> -----------------------------------------------------------
> #!/bin/bash
> #$ -S /bin/bash
> #$ -N uhv_pot
> #$ -cwd
> #$ -q UI
> #$ -l std_mem
> #$ -pe 16cpn 16
>
> module load espresso/5.1.1
> BIN_DIR=/opt/quantum-espresso/5.1.1/
>
> temp=$PWD/temp
> mkdir -p $temp
>
> results=$PWD/results
> mkdir -p $results
>
> cat > Fe2O3.scf.in <<EOF
> &CONTROL
> calculation = 'scf',
> pseudo_dir = '/Users/xhuang3/pwf/',
> outdir='$temp/',
> prefix = 'Fe2O3',
> /
> &SYSTEM
> ibrav = 4,
> celldm(1) = 9.536271655,
> celldm(3) = 6.000000000,
> nat = 30,
> ntyp = 3,
> ecutwfc = 35,
> ecutrho = 280,
> occupations = 'smearing',
> smearing = 'mp',
> degauss = 0.02,
> nspin = 2,
> starting_magnetization(1) = 0.5,
> starting_magnetization(2) = -0.5,
> /
> &ELECTRONS
> mixing_beta = 0.4,
> conv_thr = 1.0d-6,
> /
> ATOMIC_SPECIES
> Fe1 1.0 Fe.pbe-nd-rrkjus.UPF
> Fe2 1.0 Fe.pbe-nd-rrkjus.UPF
> O 1.0 O.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {crystal}
> Fe1 0.333333330 0.333333330 0.019799034
> Fe2 0.666666670 0.000000000 0.060629428
> Fe2 0.000000000 0.666666670 0.075292861
> Fe1 0.333333330 0.333333330 0.135189943
> Fe1 0.666666670 0.000000000 0.155817104
> Fe2 0.000000000 0.666666670 0.210485936
> Fe2 0.333333330 0.333333330 0.232350369
> Fe1 0.666666670 0.000000000 0.287045648
> Fe1 0.000000000 0.666666670 0.307656149
> Fe2 0.333333330 0.333333330 0.367558597
> Fe2 0.666666670 0.000000000 0.382170005
> Fe1 0.000000000 0.666666670 0.423088504
> O -0.008926107 -0.020983988 0.031308650
> O 0.321275458 0.675592765 0.031308650
> O 0.687650647 0.345391225 0.031308650
> O -0.021172740 0.313345511 0.106625540
> O 0.667851616 0.687839421 0.106625540
> O 0.353321125 -0.001184934 0.106625540
> O 0.024534827 0.024970890 0.183306362
> O 0.333769369 0.642131830 0.183306362
> O 0.641695804 0.332897279 0.183306362
> O -0.000469120 0.357826954 0.259526509
> O 0.691629403 0.667135802 0.259526509
> O 0.308839717 -0.024962756 0.259526509
> O -0.019998485 0.001310105 0.336192461
> O 0.354641930 0.686665178 0.336192461
> O 0.665356554 0.312024717 0.336192461
> O 0.012004812 0.324454789 0.411508891
> O 0.645783306 0.654661835 0.411508891
> O 0.342211883 0.020883376 0.411508891
> K_POINTS (automatic)
> 4 4 1 1 1 1
> EOF
>
> mpirun -n 16 $BIN_DIR/pw.x < Fe2O3.scf.in > Fe2O3.scf.out
>
> cat > Fe2O3.pp.in <<EOF
> &inputpp
> prefix = 'Fe2O3'
> outdir='$temp/',
> filplot = 'Fe2O3.potential'
> plot_num = 1
> /
> EOF
>
> mpirun -n 16 $BIN_DIR/pp.x < Fe2O3.pp.in > Fe2O3.pp.out
>
> ### average calculation
> cat > Fe2O3.avg.in <<EOF
> 1
> Fe2O3.potential
> 1.0d0
> 480
> 3
> 4.000000
> EOF
>
> mpirun -n 16 $BIN_DIR/average.x < Fe2O3.avg.in > Fe2O3.avg.out
>
> mv Fe2O3.* $results/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
> http://pwscf.org/mailman/listinfo/pw_forum
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it<mailto:giovanni.cantele at spin.cnr.it>
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
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> ------------------------------
>
> Message: 5
> Date: Wed, 23 Sep 2015 13:07:34 -0700
> From: reza vatan <rezavatan64 at gmail.com>
> Subject: [Pw_forum] Temperature effect on band gap
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CA+GC1EQGu3Do2Bxd8Uvea6q0K6hNz2fnaUjyk=9=
> s1q93RMfjQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm trying to use QE to see the effect of temperature on the band gap of a
> material. So I just wanted to if there is any way to include the
> temperature in electronic structure calculations using QE.
>
> Thanks in advance.
>
> Reza Vatan Meidanshahi
> Electrical Engineering Department
> Arizona State University
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> ------------------------------
>
> Message: 6
> Date: Thu, 24 Sep 2015 04:48:59 +0000 (UTC)
> From: Jaret Qi <jaretqi at yahoo.com>
> Subject: [Pw_forum] tetragonal lamno3
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <1898191297.194563.1443070139515.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear qe users,i'm trying to study a tetragonal LaMnO3 but so far not
> getting the correct structure. I am wonder if anyone of you have such input
> file.
> thank you in advance!
> Jaret
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> ------------------------------
>
> Message: 7
> Date: Thu, 24 Sep 2015 02:20:19 -0400
> From: Cameron Foss <cjfoss at umass.edu>
> Subject: [Pw_forum] Monolayer MoS2 band Structure
> To: pw_forum at pwscf.org
> Message-ID:
> <
> CANUcA0M-6GzLXMS8MBQSXdJq6AUGfhQHhkpmmO6x+jikQWdVXg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> I am attempting to obtain the band structure of monolayer MoS2, however my
> results so far do not agree well with what has been documented for
> monolayer (ML) MoS2. I consistently get an indirect band gap for ML MoS2
> caused by the 'Q-valley' minimum seen in bulk MoS2.
>
> I have tested the code with interplanar distances of 15 and 30 angstroms to
> eliminate any interplanar interactions. There have been several papers that
> report the band structure for ML MoS2 from first principles, they have used
> functionals from LDA, GGA, and an HSE hybrid functional. My best success
> has been with GGA-PW91(see input file below). Note in all my simulations I
> have measured a band gap of ~1.9eV which is in agreement with reported
> values.
>
> I am uncertain as to what the issue could be? I have tested 3 different
> PPs.
>
> %%%%%%%%%%%%%%%%%%%%
> Details on simulations:
>
> Specifically, my simulations continue to show that the 'Q-valley' is
> slightly lower (16meV~30meV) than the minimum at the K point, suggesting an
> indirect band gap. However ML mos2 has been widely shown to have a direct
> band gap at the K point where this 'Q-valley' along the conduction band is
> suppressed above the K-point minimum.
>
> I run a scf (pw.x) calculation first, followed by an nscf (pw.x) run, and a
> bands calculation with pw.x (and of course bands.x to retrieve the energy
> values). I specify 16 bands for nbnd, kpoints along symmetry paths, and a
> MP grid of 8x8x1 with a 1 1 1 offset.
>
> Input file:
>
> &control
> calculation='scf' !nscf, then bands
> restart_mode='from_scratch',
> !pseudo_dir='directory where pseudopotentials are stored/',
> !outdir='directory where large files are written/'
> pseudo_dir='/home/cameron/QE/espresso-5.1/pseudo/',
> outdir='/home/cameron/QE/espresso-5.1/2dout'
> prefix='mos2-gga',
> /
> &system
> ibrav=4, celldm(1)=5.8364, celldm(3)=10,
> nat=3, ntyp=2, ecutwfc =70, ecutrho=300 ! specified nbnd=16
> /
> &electrons
> conv_thr = 1.0d-15 ! reduced to 1.0d--12 for nscf,
> bands
> mixing_beta = 0.5 ! increased to 0.7 for nscf,
> bands
> /
> ATOMIC_SPECIES
> Mo 95.94 Mo.pw91-n-van.UPF
> S 32.065 S.pw91-n-mt.UPF
> ATOMIC_POSITIONS bohr
> S 0.00002 -0.00001 0.000000000
> Mo 2.91822 1.68481 2.929886569
> S 0.00002 -0.00001 5.859870374
> K_POINTS automatic
> 8 8 1 1 1 1
>
> I ran into some convergence issues with all the bands with this conv_thr in
> the nscf and bands calculations, so i had to reduce it to 1.0d-12 for those
> calculations. I also used a mixing beta of 0.7 for both the nscf and bands
> calculations. I am uncertain as to whether changing mixing_beta's between
> calculations is of importance or not as well, but I do not think this is
> the case.
>
> Best regards,
> Cameron
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> ------------------------------
>
> Message: 8
> Date: Thu, 24 Sep 2015 09:59:39 +0200
> From: Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr>
> Subject: Re: [Pw_forum] Temperature effect on band gap
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <9751947.cFRM24mjb0 at paulaxps>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Wednesday, September 23, 2015 01:07:34 PM reza vatan wrote:
> > I'm trying to use QE to see the effect of temperature on the band gap of
> a
> > material. So I just wanted to if there is any way to include the
> > temperature in electronic structure calculations using QE.
>
> Dear Reza,
> with some possible exception in extreme cases, the gap does not depend on
> the
> "electronic" temperature, even a high temperature correspond to a smearing
> of
> the Fermi-Dirac occupation which is much smaller than what we normally use
> to
> ease convergence in metallic systems.
>
> On the other hand, the band gap can depend on the temperature via the
> lattice
> expansion. To have a rough idea, apply the experimental lattice expansion
> to
> the zero-temperature DFT lattice, repeat the scf and bands calculation,
> check
> how the band structure changes.
>
> kind regards
>
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Universit? Paris 6
> +33 (0)1 44 275 084 / skype: paulatz
> http://www.impmc.upmc.fr/~paulatto/
> 23-24/4?16 Bo?te courrier 115
> 4 place Jussieu 75252 Paris C?dex 05
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 24 Sep 2015 10:43:18 +0200
> From: Cristian Degli Esposti Boschi <degliesposti at bo.imm.cnr.it>
> Subject: [Pw_forum] Mean internal potential for e-microscopy
> To: pw_forum at pwscf.org
> Message-ID: <5603B7A6.8020002 at bo.imm.cnr.it>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear users and developers,
>
> I have two related questions about what would be more meaningful to
> extract from a SCF calculation with DFT in Quantum Espresso as far as
> the *mean internal potential* is concerned.
>
> This quantity, in electron microscopy experiments, is linearly related
> (at least in first approx) to the response of the electron beam passing
> through a sample. In developing the theory of the response one uses the
> single particle static electic potential felt by the electrons given, in
> turn, by the solution of the Poisson equation for the total charge
> existing in the interior of the sample.
>
> Now:
>
> a. I wonder if the the DFT setting one has to use the Kohn-Sham
> potential (as "best" single body potential in the many-body problem)
> or only the contributions coming from ions + Hartree term coming from
> the electronic charge. In a series of papers of the '90s o 2000s I have
> seen that they use the second option. The rationale would be that the
> electrons from the beam at high energy are not really a part of the
> sample and are not correlated with the ones of the interior. Would you
> agree?
>
> b. Again in those papers they choose *linear augumented plane wave full
> potential*.
> Why should one use PAW? In which sense full potentials? Aren't Pseudos
> sufficient?
>
> Thanks a lot for your time.
> --
> Cristian Degli Esposti Boschi
> CNR-IMM, Sezione di Bologna,
> via Gobetti, 101, 40129, Bologna, Italia
> tel. ++39 051 6399152, fax ++39 051 6399216
> email: degliesposti -AT- bo.imm.cnr.it
> web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 24 Sep 2015 10:47:37 +0200
> From: Thomas Brumme <thomas.brumme at mpsd.mpg.de>
> Subject: Re: [Pw_forum] Monolayer MoS2 band Structure
> To: <pw_forum at pwscf.org>
> Message-ID: <5603B8A9.2020002 at mpsd.mpg.de>
> Content-Type: text/plain; charset="windows-1252"
>
> Hey Cameron,
>
> I think that the main problem is your lattice parameter.
> You use 5.8364 bohr which is 5.8364*0.529177 = 3.088 Angstrom.
> Thus, your MoS2 is under compressive strain. That's why you
> (correctly) get an indirect band gap between K and Q.
> See also Fig. 3(b) of Phys. Rev. B 85, 033305:
>
> http://journals.aps.org/prb/abstract/10.1103/PhysRevB.85.033305
>
> Cheerio
>
> Thomas
>
> On 09/24/2015 08:20 AM, Cameron Foss wrote:
> > Hello,
> >
> > I am attempting to obtain the band structure of monolayer MoS2,
> > however my results so far do not agree well with what has been
> > documented for monolayer (ML) MoS2. I consistently get an indirect
> > band gap for ML MoS2 caused by the 'Q-valley' minimum seen in bulk MoS2.
> >
> > I have tested the code with interplanar distances of 15 and 30
> > angstroms to eliminate any interplanar interactions. There have been
> > several papers that report the band structure for ML MoS2 from first
> > principles, they have used functionals from LDA, GGA, and an HSE
> > hybrid functional. My best success has been with GGA-PW91(see input
> > file below). Note in all my simulations I have measured a band gap of
> > ~1.9eV which is in agreement with reported values.
> >
> > I am uncertain as to what the issue could be? I have tested 3
> > different PPs.
> >
> > %%%%%%%%%%%%%%%%%%%%
> > Details on simulations:
> >
> > Specifically, my simulations continue to show that the 'Q-valley' is
> > slightly lower (16meV~30meV) than the minimum at the K point,
> > suggesting an indirect band gap. However ML mos2 has been widely shown
> > to have a direct band gap at the K point where this 'Q-valley' along
> > the conduction band is suppressed above the K-point minimum.
> >
> > I run a scf (pw.x) calculation first, followed by an nscf (pw.x) run,
> > and a bands calculation with pw.x (and of course bands.x to retrieve
> > the energy values). I specify 16 bands for nbnd, kpoints along
> > symmetry paths, and a MP grid of 8x8x1 with a 1 1 1 offset.
> >
> > Input file:
> >
> > &control
> > calculation='scf' !nscf, then bands
> > restart_mode='from_scratch',
> > !pseudo_dir='directory where pseudopotentials are stored/',
> > !outdir='directory where large files are written/'
> > pseudo_dir='/home/cameron/QE/espresso-5.1/pseudo/',
> > outdir='/home/cameron/QE/espresso-5.1/2dout'
> > prefix='mos2-gga',
> > /
> > &system
> > ibrav=4, celldm(1)=5.8364, celldm(3)=10,
> > nat=3, ntyp=2, ecutwfc =70, ecutrho=300 ! specified nbnd=16
> > /
> > &electrons
> > conv_thr = 1.0d-15 ! reduced to 1.0d--12 for
> > nscf, bands
> > mixing_beta = 0.5 ! increased to 0.7 for nscf,
> > bands
> > /
> > ATOMIC_SPECIES
> > Mo 95.94 Mo.pw91-n-van.UPF
> > S 32.065 S.pw91-n-mt.UPF
> > ATOMIC_POSITIONS bohr
> > S 0.00002 -0.00001 0.000000000
> > Mo 2.91822 1.68481 2.929886569
> > S 0.00002 -0.00001 5.859870374
> > K_POINTS automatic
> > 8 8 1 1 1 1
> >
> > I ran into some convergence issues with all the bands with this
> > conv_thr in the nscf and bands calculations, so i had to reduce it to
> > 1.0d-12 for those calculations. I also used a mixing beta of 0.7 for
> > both the nscf and bands calculations. I am uncertain as to whether
> > changing mixing_beta's between calculations is of importance or not as
> > well, but I do not think this is the case.
> >
> > Best regards,
> > Cameron
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Dr. rer. nat. Thomas Brumme
> Max Planck Institute for the Structure and Dynamics of Matter
> Luruper Chaussee 149
> 22761 Hamburg
>
> Tel: +49 (0)40 8998 6557
>
> email: Thomas.Brumme at mpsd.mpg.de
>
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> ------------------------------
>
> Message: 11
> Date: Thu, 24 Sep 2015 10:48:57 +0200
> From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> Subject: Re: [Pw_forum] Monolayer MoS2 band Structure
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <0806883C-F7ED-4D60-BBEC-568735A4FD84 at spin.cnr.it>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Cameron,
>
> I don?t think that this strange behavior is due to mixing_beta or
> conv_thr, so you can remove those flags from the input. Moreover, the
> vacuum space you use (~27 A) is a bit large, you can slightly reduce it to
> speedup the calculation.
>
> As far as I can see you should: 1) check if the lattice parameter is
> correct, for some materials it can happen that if you use a lattice
> parameter quite different from the equilibrium one the band structure
> undergoes more or less significant changes; 2) check your k-point path, are
> you sure you gave the correct k-points in the correct units? Maybe seeing
> the input for the nscf calculation would be useful as well.
>
> Finally, even though I do not think that this might affect your band
> structure calculation, if you include one or more ultrasoft pseudo
> potentials in you calculations, as you do, typical values of ecutrho,
> depending on the atomic element and on the pseudo potential, can range from
> ~ 6*ecutwfc to even 12*ecutwfc, so your choice 300 Ry ~ 4.3 * 70 Ry might
> produce not fully converged results.
>
> Last, if I were you, I would replace the norm conserving pseudo potential
> for S with an ultrasoft pseudo potential, which allows you to use much
> lower values of ecutwfc.
>
> I attach a band structure of monolayer MoS2 that has been done using QE
> 5.2.0, where the direct gap at K (~1.74 eV) is evident.
>
> Giovanni
>
>
>
> > On 24 Sep 2015, at 08:20, Cameron Foss <cjfoss at umass.edu> wrote:
> >
> > Hello,
> >
> > I am attempting to obtain the band structure of monolayer MoS2, however
> my results so far do not agree well with what has been documented for
> monolayer (ML) MoS2. I consistently get an indirect band gap for ML MoS2
> caused by the 'Q-valley' minimum seen in bulk MoS2.
> >
> > I have tested the code with interplanar distances of 15 and 30 angstroms
> to eliminate any interplanar interactions. There have been several papers
> that report the band structure for ML MoS2 from first principles, they have
> used functionals from LDA, GGA, and an HSE hybrid functional. My best
> success has been with GGA-PW91(see input file below). Note in all my
> simulations I have measured a band gap of ~1.9eV which is in agreement with
> reported values.
> >
> > I am uncertain as to what the issue could be? I have tested 3 different
> PPs.
> >
> > %%%%%%%%%%%%%%%%%%%%
> > Details on simulations:
> >
> > Specifically, my simulations continue to show that the 'Q-valley' is
> slightly lower (16meV~30meV) than the minimum at the K point, suggesting an
> indirect band gap. However ML mos2 has been widely shown to have a direct
> band gap at the K point where this 'Q-valley' along the conduction band is
> suppressed above the K-point minimum.
> >
> > I run a scf (pw.x) calculation first, followed by an nscf (pw.x) run,
> and a bands calculation with pw.x (and of course bands.x to retrieve the
> energy values). I specify 16 bands for nbnd, kpoints along symmetry paths,
> and a MP grid of 8x8x1 with a 1 1 1 offset.
> >
> > Input file:
> >
> > &control
> > calculation='scf' !nscf, then bands
> > restart_mode='from_scratch',
> > !pseudo_dir='directory where pseudopotentials are stored/',
> > !outdir='directory where large files are written/'
> > pseudo_dir='/home/cameron/QE/espresso-5.1/pseudo/',
> > outdir='/home/cameron/QE/espresso-5.1/2dout'
> > prefix='mos2-gga',
> > /
> > &system
> > ibrav=4, celldm(1)=5.8364, celldm(3)=10,
> > nat=3, ntyp=2, ecutwfc =70, ecutrho=300 ! specified nbnd=16
> > /
> > &electrons
> > conv_thr = 1.0d-15 ! reduced to 1.0d--12 for
> nscf, bands
> > mixing_beta = 0.5 ! increased to 0.7 for nscf,
> bands
> > /
> > ATOMIC_SPECIES
> > Mo 95.94 Mo.pw91-n-van.UPF
> > S 32.065 S.pw91-n-mt.UPF
> > ATOMIC_POSITIONS bohr
> > S 0.00002 -0.00001 0.000000000
> > Mo 2.91822 1.68481 2.929886569
> > S 0.00002 -0.00001 5.859870374
> > K_POINTS automatic
> > 8 8 1 1 1 1
> >
> > I ran into some convergence issues with all the bands with this conv_thr
> in the nscf and bands calculations, so i had to reduce it to 1.0d-12 for
> those calculations. I also used a mixing beta of 0.7 for both the nscf and
> bands calculations. I am uncertain as to whether changing mixing_beta's
> between calculations is of importance or not as well, but I do not think
> this is the case.
> >
> > Best regards,
> > Cameron
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
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>
> _______________________________________________
> Pw_forum mailing list
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>
> End of Pw_forum Digest, Vol 98, Issue 24
> ****************************************
>
>
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