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 <[email protected]>: > Send Pw_forum mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://pwscf.org/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > 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 <[email protected]> > Subject: Re: [Pw_forum] ibrav = 13 monoclinic-base-centered unique > axis > To: [email protected] > Message-ID: <[email protected]> > 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 > > [email protected] > > 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: [email protected] > > > > > ------------------------------ > > Message: 2 > Date: Wed, 23 Sep 2015 09:38:36 -0300 > From: Juliana Mendes <[email protected]> > Subject: [Pw_forum] error in charge density difference (chden.f90) > To: pw_forum <[email protected]> > Message-ID: > < > cagjdpkr5uzygux7m4fjdrjced6dedhb_0uto8zpdhjh2mss...@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150923/6179190c/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 23 Sep 2015 15:15:06 +0200 > From: Paolo Giannozzi <[email protected]> > Subject: Re: [Pw_forum] error in charge density difference (chden.f90) > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCuVk9HK62OENxoT5-mLTRGgh2DoGFH= > [email protected]> > 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 < > [email protected]> 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 > > [email protected] > > 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 -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150923/1846614d/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 23 Sep 2015 15:45:40 +0000 > From: "Huang, Xu" <[email protected]> > Subject: Re: [Pw_forum] Problem in average.x > To: PWSCF Forum <[email protected]> > Message-ID: > <[email protected]> > 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: [email protected] [[email protected]] on behalf > of Giovanni Cantele [[email protected]] > 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 <[email protected]<mailto: > [email protected]>> 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 > [email protected]<mailto:[email protected]> > 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: [email protected]<mailto:[email protected]> > Phone: +39 081 676910 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150923/2193a232/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 23 Sep 2015 13:07:34 -0700 > From: reza vatan <[email protected]> > Subject: [Pw_forum] Temperature effect on band gap > To: PWSCF Forum <[email protected]> > Message-ID: > <CA+GC1EQGu3Do2Bxd8Uvea6q0K6hNz2fnaUjyk=9= > [email protected]> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150923/e8cf8af2/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Thu, 24 Sep 2015 04:48:59 +0000 (UTC) > From: Jaret Qi <[email protected]> > Subject: [Pw_forum] tetragonal lamno3 > To: PWSCF Forum <[email protected]> > Message-ID: > <[email protected]> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150924/f96e6b79/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Thu, 24 Sep 2015 02:20:19 -0400 > From: Cameron Foss <[email protected]> > Subject: [Pw_forum] Monolayer MoS2 band Structure > To: [email protected] > Message-ID: > < > canuca0m-6gzlxms8mbqsxdjq6augfhqhhkpmmo6x+jikqwd...@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150924/b72ca68b/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Thu, 24 Sep 2015 09:59:39 +0200 > From: Lorenzo Paulatto <[email protected]> > Subject: Re: [Pw_forum] Temperature effect on band gap > To: PWSCF Forum <[email protected]> > Message-ID: <9751947.cFRM24mjb0@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 <[email protected]> > Subject: [Pw_forum] Mean internal potential for e-microscopy > To: [email protected] > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: Re: [Pw_forum] Monolayer MoS2 band Structure > To: <[email protected]> > Message-ID: <[email protected]> > 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 > > [email protected] > > 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: [email protected] > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150924/7fc93bbf/attachment-0001.html > > ------------------------------ > > Message: 11 > Date: Thu, 24 Sep 2015 10:48:57 +0200 > From: Giovanni Cantele <[email protected]> > Subject: Re: [Pw_forum] Monolayer MoS2 band Structure > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> 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 > > [email protected] > > 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: [email protected] > Phone: +39 081 676910 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150924/3a2b65ec/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 1d_2--MoS2_1L_ecut45_ecutrho455_kpt8x8x1-GM-M-K-GM.bands.png > Type: image/png > Size: 26149 bytes > Desc: not available > Url : > http://pwscf.org/pipermail/pw_forum/attachments/20150924/3a2b65ec/attachment-0001.png > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 98, Issue 24 > **************************************** > >
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